See the 'PackageToVendor' constant -- set it to decide which pkg to "vendor"/embed locally. References indeed appear to be kept completely intact.

EmbedPackageToLocal.cs

#if UNITY_EDITOR
using System;
using System.Collections;
using System.Collections.Generic;
using UnityEditor;
using UnityEditor.PackageManager.Requests;
using UnityEditor.PackageManager;
using UnityEngine;

namespace Unity.Editor.Example {
	static class EmbedPackageExample {
		private const string PackageToVendor = "com.unity.addressables";

		private static string targetPackage = null;
		private static EmbedRequest Request;
		private static ListRequest LRequest;

		[MenuItem("Window/Embed Package '"+ PackageToVendor+"'")]
		static void GetPackageName() {
			// First get the name of an installed package
			LRequest = Client.List();
			EditorApplication.update += LProgress;
			targetPackage = null;
		}

		static void LProgress() {
			if (LRequest.IsCompleted) {
				if (LRequest.Status == StatusCode.Success) {
					foreach (var package in LRequest.Result) {
						// Only retrieve packages that are currently installed in the
						// project (and are neither Built-In nor already Embedded)
						if (package.isDirectDependency && package.source != PackageSource.BuiltIn &&
							package.source != PackageSource.Embedded) {

							if (package.name == PackageToVendor) {
								Debug.LogFormat("FOUND IT:  {0}", package.name);
								targetPackage = package.name;
								break;
							}

						}
					}

				} else {
					Debug.LogError(LRequest.Error.message);
				}

				// Stop Updating
				EditorApplication.update -= LProgress;

				if (targetPackage == null || targetPackage != null && targetPackage != PackageToVendor) {
					Debug.LogErrorFormat("Unable to find targetPackage:  {0}", PackageToVendor);
				} else {
					Debug.LogFormat("Going to Vendor Package NOW:  {0} ", targetPackage);
					Embed(targetPackage);

				}

			}
		}

		static void Embed(string inTarget) {
			// Embed a package in the project
			Debug.Log("Embed('" + inTarget + "') called");
			Request = Client.Embed(inTarget);
			EditorApplication.update += Progress;

		}

		static void Progress() {
			if (Request.IsCompleted) {
				if (Request.Status == StatusCode.Success)
					Debug.Log("Embedded: " + Request.Result.packageId);
				else if (Request.Status >= StatusCode.Failure)
					Debug.Log(Request.Error.message);

				EditorApplication.update -= Progress;
			}
		}
	}
}
#endif