### 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)

RenderListParameters render_list_params(render_list[RENDER_LIST_SECONDARY].elements.ptr(), render_list[RENDER_LIST_SECONDARY].element_info.ptr(), render_list[RENDER_LIST_SECONDARY].elements.size(), false, pass_mode, rp_uniform_set, 0);
		_render_list_with_threads(&render_list_params, p_fb, RD::INITIAL_ACTION_CLEAR, RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CLEAR, RD::FINAL_ACTION_READ);
	}
	RD::get_singleton()->draw_command_end_label();
}
void RenderForwardMobile::base_uniforms_changed() {
	if (!render_base_uniform_set.is_null() && RD::get_singleton()->uniform_set_is_valid(render_base_uniform_set)) {
		RD::get_singleton()->free(render_base_uniform_set);
	}
	render_base_uniform_set = RID();
}
void RenderForwardMobile::_update_render_base_uniform_set() {
	RendererRD::LightStorage *light_storage = RendererRD::LightStorage::get_singleton();
	RendererRD::MaterialStorage *material_storage = RendererRD::MaterialStorage::get_singleton();
	if (render_base_uniform_set.is_null() || !RD::get_singleton()->uniform_set_is_valid(render_base_uniform_set) || (lightmap_texture_array_version != light_storage->lightmap_array_get_version())) {
		if (render_base_uniform_set.is_valid() && RD::get_singleton()->uniform_set_is_valid(render_base_uniform_set)) {
			RD::get_singleton()->free(render_base_uniform_set);
		}
		
		lightmap_texture_array_version = light_storage->lightmap_array_get_version();
		Vector<RD::Uniform> uniforms;
		{
			Vector<RID> ids;
			ids.resize(12);
			RID *ids_ptr = ids.ptrw();
			ids_ptr[0] = material_storage->sampler_rd_get_default(RS::CANVAS_ITEM_TEXTURE_FILTER_NEAREST, RS::CANVAS_ITEM_TEXTURE_REPEAT_DISABLED);
			ids_ptr[1] = material_storage->sampler_rd_get_default(RS::CANVAS_ITEM_TEXTURE_FILTER_LINEAR, RS::CANVAS_ITEM_TEXTURE_REPEAT_DISABLED);
			ids_ptr[2] = material_storage->sampler_rd_get_default(RS::CANVAS_ITEM_TEXTURE_FILTER_NEAREST_WITH_MIPMAPS, RS::CANVAS_ITEM_TEXTURE_REPEAT_DISABLED);
			ids_ptr[3] = material_storage->sampler_rd_get_default(RS::CANVAS_ITEM_TEXTURE_FILTER_LINEAR_WITH_MIPMAPS, RS::CANVAS_ITEM_TEXTURE_REPEAT_DISABLED);