### 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)

render_texture = light_storage->get_cubemap(shadow_size / 2);
				render_fb = light_storage->get_cubemap_fb(shadow_size / 2, p_pass);
				light_projection = light_storage->light_instance_get_shadow_camera(p_light, p_pass);
				light_transform = light_storage->light_instance_get_shadow_transform(p_light, p_pass);
				render_cubemap = true;
				finalize_cubemap = p_pass == 5;
				atlas_fb = light_storage->shadow_atlas_get_fb(p_shadow_atlas);
				atlas_size = shadow_atlas_size;
				if (p_pass == 0) {
					_render_shadow_begin();
				}
			} else {
				atlas_rect.position.x += 1;
				atlas_rect.position.y += 1;
				atlas_rect.size.x -= 2;
				atlas_rect.size.y -= 2;
				atlas_rect.position += p_pass * atlas_rect.size * dual_paraboloid_offset;
				light_projection = light_storage->light_instance_get_shadow_camera(p_light, 0);
				light_transform = light_storage->light_instance_get_shadow_transform(p_light, 0);
				using_dual_paraboloid = true;
				using_dual_paraboloid_flip = p_pass == 1;
				render_fb = light_storage->shadow_atlas_get_fb(p_shadow_atlas);
				flip_y = true;
			}
		} else if (light_storage->light_get_type(base) == RS::LIGHT_SPOT) {
			light_projection = light_storage->light_instance_get_shadow_camera(p_light, 0);
			light_transform = light_storage->light_instance_get_shadow_transform(p_light, 0);
			render_fb = light_storage->shadow_atlas_get_fb(p_shadow_atlas);
			flip_y = true;
		}