### 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)

MeshInstance *mi = mesh_instance_owner.get_or_null(p_mesh_instance);
		ERR_FAIL_COND(!mi);
		Mesh *mesh = mi->mesh;
		ERR_FAIL_UNSIGNED_INDEX(p_surface_index, mesh->surface_count);
		MeshInstance::Surface *mis = &mi->surfaces[p_surface_index];
		Mesh::Surface *s = mesh->surfaces[p_surface_index];
		s->version_lock.lock();
		
		for (uint32_t i = 0; i < mis->version_count; i++) {
			if (mis->versions[i].input_mask != p_input_mask) {
				continue;
			}
			
			r_vertex_format = mis->versions[i].vertex_format;
			r_vertex_array_rd = mis->versions[i].vertex_array;
			s->version_lock.unlock();
			return;
		}
		uint32_t version = mis->version_count;
		mis->version_count++;
		mis->versions = (Mesh::Surface::Version *)memrealloc(mis->versions, sizeof(Mesh::Surface::Version) * mis->version_count);
		_mesh_surface_generate_version_for_input_mask(mis->versions[version], s, p_input_mask, mis);
		r_vertex_format = mis->versions[version].vertex_format;
		r_vertex_array_rd = mis->versions[version].vertex_array;
		s->version_lock.unlock();
	}
	_FORCE_INLINE_ RID mesh_get_default_rd_buffer(DefaultRDBuffer p_buffer) {