### 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)

if (light_storage->owns_reflection_probe_instance(p_render_data->reflection_probe)) {
		current_cluster_builder = light_storage->reflection_probe_instance_get_cluster_builder(p_render_data->reflection_probe, &cluster_builder_shared);
		if (p_render_data->camera_attributes.is_valid()) {
			light_storage->reflection_probe_set_baked_exposure(light_storage->reflection_probe_instance_get_probe(p_render_data->reflection_probe), RSG::camera_attributes->camera_attributes_get_exposure_normalization_factor(p_render_data->camera_attributes));
		}
	} else if (rb_data.is_valid()) {
		current_cluster_builder = rb_data->cluster_builder;
		p_render_data->voxel_gi_count = 0;
		if (rb->has_custom_data(RB_SCOPE_SDFGI)) {
			Ref<RendererRD::GI::SDFGI> sdfgi = rb->get_custom_data(RB_SCOPE_SDFGI);
			if (sdfgi.is_valid()) {
				sdfgi->update_cascades();
				sdfgi->pre_process_gi(p_render_data->scene_data->cam_transform, p_render_data);
				sdfgi->update_light();
			}
		}
		gi.setup_voxel_gi_instances(p_render_data, p_render_data->render_buffers, p_render_data->scene_data->cam_transform, *p_render_data->voxel_gi_instances, p_render_data->voxel_gi_count);
	} else {
		ERR_PRINT("No render buffer nor reflection atlas, bug"); 
		current_cluster_builder = nullptr;
	}
	if (current_cluster_builder != nullptr) {
		p_render_data->cluster_buffer = current_cluster_builder->get_cluster_buffer();
		p_render_data->cluster_size = current_cluster_builder->get_cluster_size();
		p_render_data->cluster_max_elements = current_cluster_builder->get_max_cluster_elements();
	}
	_update_vrs(rb);
	RENDER_TIMESTAMP("Setup 3D Scene");
	
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_MOTION_VECTORS) {