### 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)

atlas_rect_norm.position /= directional_shadow_size;
		atlas_rect_norm.size /= directional_shadow_size;
		light_storage->light_instance_set_directional_shadow_atlas_rect(p_light, p_pass, atlas_rect_norm);
		zfar = RSG::light_storage->light_get_param(base, RS::LIGHT_PARAM_RANGE);
		render_fb = light_storage->direction_shadow_get_fb();
		render_texture = RID();
		flip_y = true;
	} else {
		
		ERR_FAIL_COND(!light_storage->owns_shadow_atlas(p_shadow_atlas));
		ERR_FAIL_COND(!light_storage->shadow_atlas_owns_light_instance(p_shadow_atlas, p_light));
		RSG::light_storage->shadow_atlas_update(p_shadow_atlas);
		uint32_t key = light_storage->shadow_atlas_get_light_instance_key(p_shadow_atlas, p_light);
		uint32_t quadrant = (key >> RendererRD::LightStorage::QUADRANT_SHIFT) & 0x3;
		uint32_t shadow = key & RendererRD::LightStorage::SHADOW_INDEX_MASK;
		uint32_t subdivision = light_storage->shadow_atlas_get_quadrant_subdivision(p_shadow_atlas, quadrant);
		ERR_FAIL_INDEX((int)shadow, light_storage->shadow_atlas_get_quadrant_shadow_size(p_shadow_atlas, quadrant));
		uint32_t shadow_atlas_size = light_storage->shadow_atlas_get_size(p_shadow_atlas);
		uint32_t quadrant_size = shadow_atlas_size >> 1;
		atlas_rect.position.x = (quadrant & 1) * quadrant_size;
		atlas_rect.position.y = (quadrant >> 1) * quadrant_size;
		uint32_t shadow_size = (quadrant_size / subdivision);
		atlas_rect.position.x += (shadow % subdivision) * shadow_size;
		atlas_rect.position.y += (shadow / subdivision) * shadow_size;
		atlas_rect.size.width = shadow_size;
		atlas_rect.size.height = shadow_size;
		zfar = light_storage->light_get_param(base, RS::LIGHT_PARAM_RANGE);
		if (light_storage->light_get_type(base) == RS::LIGHT_OMNI) {
			bool wrap = (shadow + 1) % subdivision == 0;
			dual_paraboloid_offset = wrap ? Vector2i(1 - subdivision, 1) : Vector2i(1, 0);