### 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)

_process_ssao(rb, p_render_data->environment, p_normal_roughness_slices, p_render_data->scene_data->view_projection);
			}
			if (p_use_ssil) {
				_process_ssil(rb, p_render_data->environment, p_normal_roughness_slices, p_render_data->scene_data->view_projection, p_render_data->scene_data->cam_transform);
			}
		}
	}
	
	RD::get_singleton()->barrier(RD::BARRIER_MASK_ALL_BARRIERS, RD::BARRIER_MASK_ALL_BARRIERS);
	if (current_cluster_builder) {
		
		
		
		
		
		current_cluster_builder->begin(p_render_data->scene_data->cam_transform, p_render_data->scene_data->cam_projection, !p_render_data->reflection_probe.is_valid());
	}
	bool using_shadows = true;
	if (p_render_data->reflection_probe.is_valid()) {
		if (!RSG::light_storage->reflection_probe_renders_shadows(light_storage->reflection_probe_instance_get_probe(p_render_data->reflection_probe))) {
			using_shadows = false;
		}
	} else {
		
		light_storage->update_reflection_probe_buffer(p_render_data, *p_render_data->reflection_probes, p_render_data->scene_data->cam_transform.affine_inverse(), p_render_data->environment);
	}
	uint32_t directional_light_count = 0;
	uint32_t positional_light_count = 0;
	light_storage->update_light_buffers(p_render_data, *p_render_data->lights, p_render_data->scene_data->cam_transform, p_render_data->shadow_atlas, using_shadows, directional_light_count, positional_light_count, p_render_data->directional_light_soft_shadows);
	texture_storage->update_decal_buffer(*p_render_data->decals, p_render_data->scene_data->cam_transform);