### 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)

MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
		return multimesh->uses_custom_data;
	}
	_FORCE_INLINE_ uint32_t multimesh_get_instances_to_draw(RID p_multimesh) const {
		MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
		if (multimesh->visible_instances >= 0) {
			return multimesh->visible_instances;
		}
		return multimesh->instances;
	}
	_FORCE_INLINE_ RID multimesh_get_3d_uniform_set(RID p_multimesh, RID p_shader, uint32_t p_set) const {
		MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
		if (multimesh == nullptr) {
			return RID();
		}
		if (!multimesh->uniform_set_3d.is_valid()) {
			if (!multimesh->buffer.is_valid()) {
				return RID();
			}
			Vector<RD::Uniform> uniforms;
			RD::Uniform u;
			u.uniform_type = RD::UNIFORM_TYPE_STORAGE_BUFFER;
			u.binding = 0;
			u.append_id(multimesh->buffer);
			uniforms.push_back(u);
			multimesh->uniform_set_3d = RD::get_singleton()->uniform_set_create(uniforms, p_shader, p_set);
		}
		return multimesh->uniform_set_3d;
	}
	_FORCE_INLINE_ RID multimesh_get_2d_uniform_set(RID p_multimesh, RID p_shader, uint32_t p_set) const {