### 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)

struct Surface {
			RID vertex_buffer;
			RID uniform_set;
			Mesh::Surface::Version *versions = nullptr; 
			uint32_t version_count = 0;
		};
		LocalVector<Surface> surfaces;
		LocalVector<float> blend_weights;
		RID blend_weights_buffer;
		List<MeshInstance *>::Element *I = nullptr; 
		uint64_t skeleton_version = 0;
		bool dirty = false;
		bool weights_dirty = false;
		SelfList<MeshInstance> weight_update_list;
		SelfList<MeshInstance> array_update_list;
		Transform2D canvas_item_transform_2d;
		MeshInstance() :
				weight_update_list(this), array_update_list(this) {}
	};
	void _mesh_surface_generate_version_for_input_mask(Mesh::Surface::Version &v, Mesh::Surface *s, uint32_t p_input_mask, MeshInstance::Surface *mis = nullptr);
	void _mesh_instance_clear(MeshInstance *mi);
	void _mesh_instance_add_surface(MeshInstance *mi, Mesh *mesh, uint32_t p_surface);
	mutable RID_Owner<MeshInstance> mesh_instance_owner;
	SelfList<MeshInstance>::List dirty_mesh_instance_weights;
	SelfList<MeshInstance>::List dirty_mesh_instance_arrays;
	
	struct MultiMesh {
		RID mesh;
		int instances = 0;
		RS::MultimeshTransformFormat xform_format = RS::MULTIMESH_TRANSFORM_3D;