### 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)

}
void RenderForwardClustered::_geometry_instance_update(RenderGeometryInstance *p_geometry_instance) {
	RendererRD::MeshStorage *mesh_storage = RendererRD::MeshStorage::get_singleton();
	RendererRD::ParticlesStorage *particles_storage = RendererRD::ParticlesStorage::get_singleton();
	GeometryInstanceForwardClustered *ginstance = static_cast<GeometryInstanceForwardClustered *>(p_geometry_instance);
	if (ginstance->data->dirty_dependencies) {
		ginstance->data->dependency_tracker.update_begin();
	}
	
	switch (ginstance->data->base_type) {
		case RS::INSTANCE_MESH: {
			const RID *materials = nullptr;
			uint32_t surface_count;
			RID mesh = ginstance->data->base;
			materials = mesh_storage->mesh_get_surface_count_and_materials(mesh, surface_count);
			if (materials) {
				
				const RID *inst_materials = ginstance->data->surface_materials.ptr();
				uint32_t surf_mat_count = ginstance->data->surface_materials.size();
				for (uint32_t j = 0; j < surface_count; j++) {
					RID material = (j < surf_mat_count && inst_materials[j].is_valid()) ? inst_materials[j] : materials[j];
					_geometry_instance_add_surface(ginstance, j, material, mesh);
				}
			}
			ginstance->instance_count = 1;
		} break;
		case RS::INSTANCE_MULTIMESH: {
			RID mesh = mesh_storage->multimesh_get_mesh(ginstance->data->base);
			if (mesh.is_valid()) {
				const RID *materials = nullptr;