Source: https://forum.unity.com/threads/one-skeleton-multiple-meshes-customization.358560/

MeshCombiner.cs

using UnityEngine;
using System.Collections.Generic;
 
using HierarchyDict = System.Collections.Generic.Dictionary<string, UnityEngine.Transform>;
using BoneTransformDict = System.Collections.Generic.Dictionary<string, utils.Tuple<UnityEngine.Transform, string>>;
 
namespace utils
{
    public class MeshCombiner
    {
#region Operations
        //! Combine mesh.
        /*!
            \return combined mesh instance.
        */
        public static GameObject Combine(List<SkinnedMeshRenderer> SkinnedRenderers)
        {
            // Generated GO
            GameObject final_mesh_go = new GameObject("Mesh");
            // Dummy parent holder
            GameObject dummy_parent = new GameObject("DummyParent");
 
            // All available bones
            var all_bones = new BoneTransformDict();
            // Traverse through all skinned mesh renderers
            foreach(var renderer in SkinnedRenderers)
            {
                var renderer_bones = renderer.bones;
                foreach (var bone in renderer_bones)
                {
                    // Bone doesn't exist, add it
                    if (!all_bones.ContainsKey(bone.name))
                        all_bones[bone.name] = new utils.Tuple<Transform, string>(bone, bone.parent.name);
                }
            }
 
            var combineInstanceArrays = new Dictionary<Material, List<CombineInstance>>();
            var bone_weights = new Dictionary<Mesh, BoneWeight[]>();
            // Map between bone name and index
            var added_bones = new Dictionary<string, int>();
            // List of child objects holding the skinned mesh renderers to be
            // destroyed when finished
            var child_objects_to_destroy = new List<GameObject>();
 
            int bone_index = 0;
            foreach(var renderer in SkinnedRenderers)
            {
                child_objects_to_destroy.Add(renderer.transform.parent.gameObject);
 
                var renderer_bones = renderer.bones;
                // Add all bones as first and save the indices of them
                foreach (var bone in renderer_bones)
                {
                    // Bone not yet added
                    if (!added_bones.ContainsKey(bone.name))
                        added_bones[bone.name] = bone_index++;
                }
                // Adjust bone weights indices based on real indices of bones
                var bone_weights_list = new BoneWeight[renderer.sharedMesh.boneWeights.Length];
                var renderer_bone_weights = renderer.sharedMesh.boneWeights;
                for (int i = 0; i < renderer_bone_weights.Length; ++i)
                {
 
                    BoneWeight current_bone_weight = renderer_bone_weights[i];
 
                    current_bone_weight.boneIndex0 = added_bones[renderer_bones[current_bone_weight.boneIndex0].name];
                    current_bone_weight.boneIndex2 = added_bones[renderer_bones[current_bone_weight.boneIndex2].name];
                    current_bone_weight.boneIndex3 = added_bones[renderer_bones[current_bone_weight.boneIndex3].name];
                    current_bone_weight.boneIndex1 = added_bones[renderer_bones[current_bone_weight.boneIndex1].name];
 
                    bone_weights_list[i] = current_bone_weight;
                }
                bone_weights[renderer.sharedMesh] = bone_weights_list;
 
                // Handle bad input
                if (renderer.sharedMaterials.Length != renderer.sharedMesh.subMeshCount)
                {
                    Debug.LogError("Mismatch between material count and submesh count. Is this the correct MeshRenderer?");
                    continue;
                }
 
                // Prepare stuff for mesh combination with same materials
                for (int i = 0; i < renderer.sharedMesh.subMeshCount; i++)
                {
                    // Material not in dict, add it
                    if (!combineInstanceArrays.ContainsKey(renderer.sharedMaterials[i]))
                        combineInstanceArrays[renderer.sharedMaterials[i]] = new List<CombineInstance>();
                    var actual_mat_list = combineInstanceArrays[renderer.sharedMaterials[i]];
                    // Add new instance
                    var combine_instance = new CombineInstance();
                    combine_instance.transform = renderer.transform.localToWorldMatrix;
                    combine_instance.subMeshIndex = i;
                    combine_instance.mesh = renderer.sharedMesh;
 
                    actual_mat_list.Add(combine_instance);
                }
                // No need to use it anymore
                renderer.enabled = false;
            }
            var bones_hierarchy = new HierarchyDict();
            // Recreate bone structure
            foreach (var bone in all_bones)
            {
                // Bone not processed, process it
                if (!bones_hierarchy.ContainsKey(bone.Key))
                    AddParent(bone.Key, bones_hierarchy, all_bones, dummy_parent);
            }
 
            // Create bone array from preprocessed dict
            var bones = new Transform[added_bones.Count];
            foreach (var bone in added_bones)
                bones[bone.Value] = bones_hierarchy[bone.Key];
 
            // Get the root bone
            Transform root_bone = bones[0];
 
            while (root_bone.parent != null)
            {
                // Get parent
                if (bones_hierarchy.ContainsKey(root_bone.parent.name))
                    root_bone = root_bone.parent;
                else
                    break;
            }
 
 
            // Create skinned mesh renderer GO
            GameObject combined_mesh_go = new GameObject("Combined");
            combined_mesh_go.transform.parent = final_mesh_go.transform;
            combined_mesh_go.transform.localPosition = Vector3.zero;
 
            // Fill bind poses
            var bind_poses = new Matrix4x4[bones.Length];
            for (int i = 0; i < bones.Length; ++i)
                bind_poses[i] = bones[i].worldToLocalMatrix * combined_mesh_go.transform.localToWorldMatrix;
 
            // Need to move it to new GO
            root_bone.parent = final_mesh_go.transform;
 
            // Combine meshes into one
            var combined_new_mesh = new Mesh();
            var combined_vertices = new List<Vector3>();
            var combined_uvs = new List<Vector2>();
            var combined_indices = new List<int[]>();
            var combined_bone_weights = new List<BoneWeight>();
            var combined_materials = new Material[combineInstanceArrays.Count];
 
            var vertex_offset_map = new Dictionary<Mesh, int>();
 
            int vertex_index_offset = 0;
            int current_material_index = 0;
 
            foreach (var combine_instance in combineInstanceArrays)
            {
                combined_materials[current_material_index++] = combine_instance.Key;
                var submesh_indices = new List<int>();
                // Process meshes for each material
                foreach (var combine in combine_instance.Value)
                {
                    // Update vertex offset for current mesh
                    if (!vertex_offset_map.ContainsKey(combine.mesh))
                    {
                        // Add vertices for mesh
                        combined_vertices.AddRange(combine.mesh.vertices);
                        // Set uvs
                        combined_uvs.AddRange(combine.mesh.uv);
                        // Add weights
                        combined_bone_weights.AddRange(bone_weights[combine.mesh]);
 
                        vertex_offset_map[combine.mesh] = vertex_index_offset;
                        vertex_index_offset += combine.mesh.vertexCount;
                    }
                    int vertex_current_offset = vertex_offset_map[combine.mesh];
 
                    var indices = combine.mesh.GetTriangles(combine.subMeshIndex);
                    // Need to "shift" indices
                    for (int k = 0; k < indices.Length; ++k)
                        indices[k] += vertex_current_offset;
 
                    submesh_indices.AddRange(indices);
                }
                // Push indices for given submesh
                combined_indices.Add(submesh_indices.ToArray());
            }
 
            combined_new_mesh.vertices = combined_vertices.ToArray();
            combined_new_mesh.uv = combined_uvs.ToArray();
            combined_new_mesh.boneWeights = combined_bone_weights.ToArray();
 
            combined_new_mesh.subMeshCount = combined_materials.Length;
            for (int i = 0; i < combined_indices.Count; ++i)
                combined_new_mesh.SetTriangles(combined_indices[i], i);
 
            // Create mesh renderer
            SkinnedMeshRenderer combined_skin_mesh_renderer = combined_mesh_go.AddComponent<SkinnedMeshRenderer>();
            combined_skin_mesh_renderer.sharedMesh = combined_new_mesh;
            combined_skin_mesh_renderer.bones = bones;
            combined_skin_mesh_renderer.rootBone = root_bone;
            combined_skin_mesh_renderer.sharedMesh.bindposes = bind_poses;
 
            combined_skin_mesh_renderer.sharedMesh.RecalculateNormals();
            combined_skin_mesh_renderer.sharedMesh.RecalculateBounds();
            combined_skin_mesh_renderer.sharedMaterials = combined_materials;
 
            // Destroy children
            foreach (var child in child_objects_to_destroy)
                GameObject.DestroyImmediate(child);
            // Destroy dummy parent
            GameObject.DestroyImmediate(dummy_parent);
 
            return final_mesh_go;
        }
 
        static void AddParent(string BoneName, HierarchyDict BoneHierarchy, BoneTransformDict AllBones, GameObject DummyParent)
        {
            Transform actual_bone = null;
            // Must be bone
            if (AllBones.ContainsKey(BoneName))
            {
                var bone_tuple = AllBones[BoneName];
                // Add parent recursively if not added
                if (!BoneHierarchy.ContainsKey(bone_tuple._2))
                {
                    AddParent(bone_tuple._2, BoneHierarchy, AllBones, DummyParent);
                    // Unparent all children of parents
                    Unparent(BoneHierarchy[bone_tuple._2], DummyParent);
                }
 
 
                bone_tuple._1.parent = BoneHierarchy[bone_tuple._2];
                actual_bone = bone_tuple._1;
            }
 
            BoneHierarchy[BoneName] = actual_bone;
        }
 
        static void Unparent(Transform Parent, GameObject DummyParent)
        {
            if (Parent != null)
            {
                var unparent_list = new List<Transform>();
 
                foreach (Transform child in Parent.transform)
                    unparent_list.Add(child);
 
                foreach (var child in unparent_list)
                    child.parent = DummyParent.transform;
            }
        }
#endregion
    }
}

Tuple.cs

public struct Tuple<T1, T2>
{
    public readonly T1 _1;
    public readonly T2 _2;

    public Tuple(T1 T1_, T2 T2_)
    {
        _1 = T1_;
        _2 = T2_;
    }
}