### 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)

RendererRD::LightStorage *light_storage = RendererRD::LightStorage::get_singleton();
	RendererRD::TextureStorage *texture_storage = RendererRD::TextureStorage::get_singleton();
	p_render_data->cube_shadows.clear();
	p_render_data->shadows.clear();
	p_render_data->directional_shadows.clear();
	Plane camera_plane(-p_render_data->scene_data->cam_transform.basis.get_column(Vector3::AXIS_Z), p_render_data->scene_data->cam_transform.origin);
	float lod_distance_multiplier = p_render_data->scene_data->cam_projection.get_lod_multiplier();
	{
		for (int i = 0; i < p_render_data->render_shadow_count; i++) {
			RID li = p_render_data->render_shadows[i].light;
			RID base = light_storage->light_instance_get_base_light(li);
			if (light_storage->light_get_type(base) == RS::LIGHT_DIRECTIONAL) {
				p_render_data->directional_shadows.push_back(i);
			} else if (light_storage->light_get_type(base) == RS::LIGHT_OMNI && light_storage->light_omni_get_shadow_mode(base) == RS::LIGHT_OMNI_SHADOW_CUBE) {
				p_render_data->cube_shadows.push_back(i);
			} else {
				p_render_data->shadows.push_back(i);
			}
		}
		
		for (const int &index : p_render_data->cube_shadows) {
			_render_shadow_pass(p_render_data->render_shadows[index].light, p_render_data->shadow_atlas, p_render_data->render_shadows[index].pass, p_render_data->render_shadows[index].instances, camera_plane, lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, true, true, true, p_render_data->render_info);
		}