Demo of https://github.com/godotengine/godot/issues/2314 and fixed workaround

ExtendsArea2D.gd

extends Area2D

func _ready():
	if get_tree().is_editor_hint():
		return
	#old_workaround()
	fixed_workaround()

func fixed_workaround():
	var children = get_children()
	get_tree().set_editor_hint(true)
	for shape in children:
		remove_child(shape)
		add_child(shape)
		if shape extends CollisionShape2D:
			shape.set_shape(shape.get_shape())
		elif shape extends CollisionPolygon2D:
			shape.set_polygon(shape.get_polygon())
	get_tree().set_editor_hint(false)

func old_workaround():
	for shape in get_children():
		get_tree().set_editor_hint(true)
		remove_child(shape)
		add_child(shape)
		get_tree().set_editor_hint(false)
		if shape extends CollisionShape2D:
			shape.set_shape(shape.get_shape())
		elif shape extends CollisionPolygon2D:
			shape.set_polygon(shape.get_polygon())
		remove_child(shape)
		add_child(shape)

ExtendsArea2D.tscn

[gd_scene load_steps=2 format=1]

[ext_resource path="res://ExtendsArea2D.gd" type="Script" id=1]

[node name="ExtendsArea2D" type="Area2D"]

input/pickable = true
gravity_vec = Vector2( 0, 1 )
gravity = 98.0
linear_damp = 0.1
angular_damp = 1.0
script/script = ExtResource( 1 )

Level.gd

extends Node2D

func _ready():
	for child in get_children():
		report_shapes(child)

func report_shapes(node):
	var shape_count = node.get_shape_count()
	print(node.get_name(), " node has ", shape_count, " collision shapes in it.")
	for index in range(0, shape_count):
		print(" - shape #", index, " = ", node.get_shape(index))

Level.tscn

[gd_scene load_steps=7 format=1]

[ext_resource path="res://Level.gd" type="Script" id=1]
[ext_resource path="res://ExtendsArea2D.tscn" type="PackedScene" id=2]

[sub_resource type="CapsuleShape2D" id=3]

custom_solver_bias = 0.0
radius = 10.0
height = 20.0

[sub_resource type="RectangleShape2D" id=4]

custom_solver_bias = 0.0
extents = Vector2( 10, 10 )

[sub_resource type="CircleShape2D" id=6]

custom_solver_bias = 0.0
radius = 10.0

[sub_resource type="CapsuleShape2D" id=5]

custom_solver_bias = 0.0
radius = 10.0
height = 20.0

[node name="TopNode" type="Node2D"]

script/script = ExtResource( 1 )

[node name="Shapes" parent="." instance=ExtResource( 2 )]

transform/pos = Vector2( 60, 0 )

[node name="CollisionShape" type="CollisionShape2D" parent="Shapes"]

shape = SubResource( 3 )
trigger = false
_update_shape_index = 0

[node name="CollisionShape2D" type="CollisionShape2D" parent="Shapes"]

transform/pos = Vector2( -8.67657, 0.695358 )
shape = SubResource( 4 )
trigger = false
_update_shape_index = 1

[node name="Polygons" parent="." instance=ExtResource( 2 )]

transform/pos = Vector2( 120, 0 )

[node name="CollisionPolygon2D" type="CollisionPolygon2D" parent="Polygons"]

build_mode = 0
polygon = Vector2Array( -15.1588, -4.15517, -12.9081, -15.5819, -3.38585, -15.5819, 5.44388, -5.88649, -6.15596, 3.11637 )
shape_range = Vector2( 0, 0 )
trigger = false

[node name="CollisionPolygon2D 2" type="CollisionPolygon2D" parent="Polygons"]

transform/pos = Vector2( -2.77011, -1.03879 )
build_mode = 0
polygon = Vector2Array( -13.0812, 4.67456, -5.46342, 9.69538, 7.34834, 4.84769, 13.9274, 18.8714, -10.3111, 20.4296 )
shape_range = Vector2( 1, 2 )
trigger = false

[node name="Mixed" parent="." instance=ExtResource( 2 )]

transform/pos = Vector2( 180, 0 )

[node name="CollisionPolygon2D" type="CollisionPolygon2D" parent="Mixed"]

build_mode = 0
polygon = Vector2Array( -15.1588, -4.15517, -12.9081, -15.5819, -3.38585, -15.5819, 5.44388, -5.88649, -6.15596, 3.11637 )
shape_range = Vector2( 0, 0 )
trigger = false

[node name="CollisionShape2D" type="CollisionShape2D" parent="Mixed"]

transform/pos = Vector2( 8.01735, -1.9436 )
shape = SubResource( 6 )
trigger = false
_update_shape_index = 1

[node name="CollisionPolygon2D 2" type="CollisionPolygon2D" parent="Mixed"]

transform/pos = Vector2( -2.77011, -1.03879 )
build_mode = 0
polygon = Vector2Array( -13.0812, 4.67456, -5.46342, 9.69538, 7.34834, 4.84769, 13.9274, 18.8714, -10.3111, 20.4296 )
shape_range = Vector2( 2, 3 )
trigger = false

[node name="Area2D" type="Area2D" parent="."]

input/pickable = true
shapes/0/shape = SubResource( 5 )
shapes/0/transform = Matrix32( 1, 0, 0, 1, 0, 0 )
shapes/0/trigger = false
gravity_vec = Vector2( 0, 1 )
gravity = 98.0
linear_damp = 0.1
angular_damp = 1.0

[node name="CollisionShape" type="CollisionShape2D" parent="Area2D"]

shape = SubResource( 5 )
trigger = false
_update_shape_index = 0