### 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)

}
	RID normal_roughness_views[RendererSceneRender::MAX_RENDER_VIEWS];
	if (rb_data.is_valid() && rb_data->has_normal_roughness()) {
		for (uint32_t v = 0; v < rb->get_view_count(); v++) {
			normal_roughness_views[v] = rb_data->get_normal_roughness(v);
		}
	}
	_pre_opaque_render(p_render_data, using_ssao, using_ssil, using_sdfgi || using_voxelgi, normal_roughness_views, rb_data.is_valid() && rb_data->has_voxelgi() ? rb_data->get_voxelgi() : RID());
	RD::get_singleton()->draw_command_begin_label("Render Opaque Pass");
	p_render_data->scene_data->directional_light_count = p_render_data->directional_light_count;
	p_render_data->scene_data->opaque_prepass_threshold = 0.0f;
	_setup_environment(p_render_data, is_reflection_probe, screen_size, !is_reflection_probe, p_default_bg_color, true);
	RENDER_TIMESTAMP("Render Opaque Pass");
	RID rp_uniform_set = _setup_render_pass_uniform_set(RENDER_LIST_OPAQUE, p_render_data, radiance_texture, true);
	bool can_continue_color = !scene_state.used_screen_texture && !using_ssr && !using_sss;
	bool can_continue_depth = !(scene_state.used_depth_texture || scene_state.used_normal_texture) && !using_ssr && !using_sss;
	{
		bool will_continue_color = (can_continue_color || draw_sky || draw_sky_fog_only || debug_voxelgis || debug_sdfgi_probes);
		bool will_continue_depth = (can_continue_depth || draw_sky || draw_sky_fog_only || debug_voxelgis || debug_sdfgi_probes);
		Vector<Color> c;
		{
			Color cc = clear_color.srgb_to_linear();
			if (using_separate_specular || rb_data.is_valid()) {
				cc.a = 0; 
			}
			c.push_back(cc);
			if (rb_data.is_valid()) {
				c.push_back(Color(0, 0, 0, 0)); 
				c.push_back(Color(0, 0, 0, 0)); 
			}