### 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)

RenderDataRD render_data;
	render_data.scene_data = &scene_data;
	render_data.cluster_size = 1;
	render_data.cluster_max_elements = 32;
	render_data.instances = &p_instances;
	_update_render_base_uniform_set();
	_setup_environment(&render_data, true, Vector2(1, 1), false, Color());
	PassMode pass_mode = PASS_MODE_DEPTH_MATERIAL;
	_fill_render_list(RENDER_LIST_SECONDARY, &render_data, pass_mode);
	render_list[RENDER_LIST_SECONDARY].sort_by_key();
	_fill_instance_data(RENDER_LIST_SECONDARY);
	RID rp_uniform_set = _setup_render_pass_uniform_set(RENDER_LIST_SECONDARY, nullptr, RID());
	RENDER_TIMESTAMP("Render 3D Material");
	{
		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(), true, pass_mode, 0, true, false, rp_uniform_set);
		
		Vector<Color> clear = {
			Color(0, 0, 0, 0),
			Color(0, 0, 0, 0),
			Color(0, 0, 0, 0),
			Color(0, 0, 0, 0),
			Color(0, 0, 0, 0)
		};
		RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(p_framebuffer, RD::INITIAL_ACTION_CLEAR, RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CLEAR, RD::FINAL_ACTION_READ, clear, 1.0, 0, p_region);
		_render_list(draw_list, RD::get_singleton()->framebuffer_get_format(p_framebuffer), &render_list_params, 0, render_list_params.element_count);
		RD::get_singleton()->draw_list_end();
	}
	RD::get_singleton()->draw_command_end_label();
}
void RenderForwardClustered::_render_uv2(const PagedArray<RenderGeometryInstance *> &p_instances, RID p_framebuffer, const Rect2i &p_region) {