### 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)

}
	
	for (int i = 0; i < (int)p_render_data->instances->size(); i++) {
		GeometryInstanceForwardMobile *inst = static_cast<GeometryInstanceForwardMobile *>((*p_render_data->instances)[i]);
		Vector3 center = inst->transform.origin;
		if (p_render_data->scene_data->cam_orthogonal) {
			if (inst->use_aabb_center) {
				center = inst->transformed_aabb.get_support(-near_plane.normal);
			}
			inst->depth = near_plane.distance_to(center) - inst->sorting_offset;
		} else {
			if (inst->use_aabb_center) {
				center = inst->transformed_aabb.position + (inst->transformed_aabb.size * 0.5);
			}
			inst->depth = p_render_data->scene_data->cam_transform.origin.distance_to(center) - inst->sorting_offset;
		}
		uint32_t depth_layer = CLAMP(int(inst->depth * 16 / z_max), 0, 15);
		uint32_t flags = inst->base_flags; 
		if (inst->non_uniform_scale) {
			flags |= INSTANCE_DATA_FLAGS_NON_UNIFORM_SCALE;
		}
		bool uses_lightmap = false;
		
		if (p_render_list == RENDER_LIST_OPAQUE) {
			if (inst->lightmap_instance.is_valid()) {
				int32_t lightmap_cull_index = -1;
				for (uint32_t j = 0; j < scene_state.lightmaps_used; j++) {
					if (scene_state.lightmap_ids[j] == inst->lightmap_instance) {
						lightmap_cull_index = j;
						break;