### 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)

static MeshStorage *get_singleton();
	MeshStorage();
	virtual ~MeshStorage();
	bool free(RID p_rid);
	RID get_default_rd_storage_buffer() const { return default_rd_storage_buffer; }
	
	bool owns_mesh(RID p_rid) { return mesh_owner.owns(p_rid); };
	virtual RID mesh_allocate() override;
	virtual void mesh_initialize(RID p_mesh) override;
	virtual void mesh_free(RID p_rid) override;
	virtual void mesh_set_blend_shape_count(RID p_mesh, int p_blend_shape_count) override;
	
	virtual void mesh_add_surface(RID p_mesh, const RS::SurfaceData &p_surface) override;
	virtual int mesh_get_blend_shape_count(RID p_mesh) const override;
	virtual void mesh_set_blend_shape_mode(RID p_mesh, RS::BlendShapeMode p_mode) override;
	virtual RS::BlendShapeMode mesh_get_blend_shape_mode(RID p_mesh) const override;
	virtual void mesh_surface_update_vertex_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) override;
	virtual void mesh_surface_update_attribute_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) override;
	virtual void mesh_surface_update_skin_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) override;
	virtual void mesh_surface_set_material(RID p_mesh, int p_surface, RID p_material) override;
	virtual RID mesh_surface_get_material(RID p_mesh, int p_surface) const override;
	virtual RS::SurfaceData mesh_get_surface(RID p_mesh, int p_surface) const override;
	virtual int mesh_get_surface_count(RID p_mesh) const override;
	virtual void mesh_set_custom_aabb(RID p_mesh, const AABB &p_aabb) override;
	virtual AABB mesh_get_custom_aabb(RID p_mesh) const override;
	virtual AABB mesh_get_aabb(RID p_mesh, RID p_skeleton = RID()) override;
	virtual void mesh_set_shadow_mesh(RID p_mesh, RID p_shadow_mesh) override;
	virtual void mesh_clear(RID p_mesh) override;
	virtual bool mesh_needs_instance(RID p_mesh, bool p_has_skeleton) override;
	_FORCE_INLINE_ const RID *mesh_get_surface_count_and_materials(RID p_mesh, uint32_t &r_surface_count) {