### 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)

uint64_t last_scene_shadow_pass = light_storage->light_instance_get_shadow_pass(p_light);
		if (last_scene_shadow_pass != get_scene_pass()) {
			light_storage->light_instance_set_directional_rect(p_light, light_storage->get_directional_shadow_rect());
			light_storage->directional_shadow_increase_current_light();
			light_storage->light_instance_set_shadow_pass(p_light, get_scene_pass());
		}
		use_pancake = light_storage->light_get_param(base, RS::LIGHT_PARAM_SHADOW_PANCAKE_SIZE) > 0;
		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);
		atlas_rect = light_storage->light_instance_get_directional_rect(p_light);
		if (light_storage->light_directional_get_shadow_mode(base) == RS::LIGHT_DIRECTIONAL_SHADOW_PARALLEL_4_SPLITS) {
			atlas_rect.size.width /= 2;
			atlas_rect.size.height /= 2;
			if (p_pass == 1) {
				atlas_rect.position.x += atlas_rect.size.width;
			} else if (p_pass == 2) {
				atlas_rect.position.y += atlas_rect.size.height;
			} else if (p_pass == 3) {
				atlas_rect.position += atlas_rect.size;
			}
		} else if (light_storage->light_directional_get_shadow_mode(base) == RS::LIGHT_DIRECTIONAL_SHADOW_PARALLEL_2_SPLITS) {
			atlas_rect.size.height /= 2;
			if (p_pass == 0) {
			} else {
				atlas_rect.position.y += atlas_rect.size.height;
			}
		}
		float directional_shadow_size = light_storage->directional_shadow_get_size();
		Rect2 atlas_rect_norm = atlas_rect;
		atlas_rect_norm.position /= directional_shadow_size;