### 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)

while (geometry_instance_dirty_list.first()) {
		_geometry_instance_update(geometry_instance_dirty_list.first()->self());
	}
}
void RenderForwardClustered::_geometry_instance_dependency_changed(Dependency::DependencyChangedNotification p_notification, DependencyTracker *p_tracker) {
	switch (p_notification) {
		case Dependency::DEPENDENCY_CHANGED_MATERIAL:
		case Dependency::DEPENDENCY_CHANGED_MESH:
		case Dependency::DEPENDENCY_CHANGED_PARTICLES:
		case Dependency::DEPENDENCY_CHANGED_MULTIMESH:
		case Dependency::DEPENDENCY_CHANGED_SKELETON_DATA: {
			static_cast<RenderGeometryInstance *>(p_tracker->userdata)->_mark_dirty();
			static_cast<GeometryInstanceForwardClustered *>(p_tracker->userdata)->data->dirty_dependencies = true;
		} break;
		case Dependency::DEPENDENCY_CHANGED_MULTIMESH_VISIBLE_INSTANCES: {
			GeometryInstanceForwardClustered *ginstance = static_cast<GeometryInstanceForwardClustered *>(p_tracker->userdata);
			if (ginstance->data->base_type == RS::INSTANCE_MULTIMESH) {
				ginstance->instance_count = RendererRD::MeshStorage::get_singleton()->multimesh_get_instances_to_draw(ginstance->data->base);
			}
		} break;
		default: {
			
		} break;
	}
}
void RenderForwardClustered::_geometry_instance_dependency_deleted(const RID &p_dependency, DependencyTracker *p_tracker) {
	static_cast<RenderGeometryInstance *>(p_tracker->userdata)->_mark_dirty();
	static_cast<GeometryInstanceForwardClustered *>(p_tracker->userdata)->data->dirty_dependencies = true;
}
RenderGeometryInstance *RenderForwardClustered::geometry_instance_create(RID p_base) {