### Godot version

v4.1.dev4.mono.official [5c2295ff5]

### System information

Godot v4.1.dev4.mono - Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti with Max-Q Design (NVIDIA; 31.0.15.3179) - Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz (12 Threads)

### Issue description

When I open my project console gets filled with these errors.

```
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
```
### Steps to reproduce (from fresh new project)
Steps to reproduce `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` error.
1. Create new project.
1.1 Godot version used: v4.1.beta2.mono.official [a2575cba4]).
1.2 I have this setting On: Editor -> Editor Settings -> General -> Interface -> Scene Tabs -> "Restore Scenes On Load".
2. Copy/Paste .glb model with a skeleton to the project folder.
3. Double click .glb file in the editor and click Reimport.
4. Right click .glb file and select New Inherited Scene.
5. Click ctrl+s to save that scene for example player.tscn.
6. Right click player.tscn and select Instantiate.
7. Save everything and restart Godot editor. When launching editor you will see message `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` in console and Output.

### Steps to reproduce (from MRP)

Open project

### Minimal reproduction project

MRP uses v4.1.beta1.mono.official [828ec2c5d], but same error still persists
[MRP.zip](https://github.com/godotengine/godot/files/11703993/MRP.zip)

virtual RID multimesh_allocate() override;
	virtual void multimesh_initialize(RID p_multimesh) override;
	virtual void multimesh_free(RID p_rid) override;
	virtual void multimesh_allocate_data(RID p_multimesh, int p_instances, RS::MultimeshTransformFormat p_transform_format, bool p_use_colors = false, bool p_use_custom_data = false) override;
	virtual int multimesh_get_instance_count(RID p_multimesh) const override;
	virtual void multimesh_set_mesh(RID p_multimesh, RID p_mesh) override;
	virtual void multimesh_instance_set_transform(RID p_multimesh, int p_index, const Transform3D &p_transform) override;
	virtual void multimesh_instance_set_transform_2d(RID p_multimesh, int p_index, const Transform2D &p_transform) override;
	virtual void multimesh_instance_set_color(RID p_multimesh, int p_index, const Color &p_color) override;
	virtual void multimesh_instance_set_custom_data(RID p_multimesh, int p_index, const Color &p_color) override;
	virtual RID multimesh_get_mesh(RID p_multimesh) const override;
	virtual Transform3D multimesh_instance_get_transform(RID p_multimesh, int p_index) const override;
	virtual Transform2D multimesh_instance_get_transform_2d(RID p_multimesh, int p_index) const override;
	virtual Color multimesh_instance_get_color(RID p_multimesh, int p_index) const override;
	virtual Color multimesh_instance_get_custom_data(RID p_multimesh, int p_index) const override;
	virtual void multimesh_set_buffer(RID p_multimesh, const Vector<float> &p_buffer) override;
	virtual Vector<float> multimesh_get_buffer(RID p_multimesh) const override;
	virtual void multimesh_set_visible_instances(RID p_multimesh, int p_visible) override;
	virtual int multimesh_get_visible_instances(RID p_multimesh) const override;
	virtual AABB multimesh_get_aabb(RID p_multimesh) const override;
	void _update_dirty_multimeshes();
	bool _multimesh_enable_motion_vectors(RID p_multimesh);
	void _multimesh_get_motion_vectors_offsets(RID p_multimesh, uint32_t &r_current_offset, uint32_t &r_prev_offset);
	_FORCE_INLINE_ RS::MultimeshTransformFormat multimesh_get_transform_format(RID p_multimesh) const {