### 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)

}
		if (using_subpass_post_process) {
			
			framebuffer = four_subpasses;
		} else if (using_subpass_transparent) {
			
			framebuffer = rb_data->get_color_fbs(RenderBufferDataForwardMobile::FB_CONFIG_THREE_SUBPASSES);
		} else {
			
			framebuffer = rb_data->get_color_fbs(RenderBufferDataForwardMobile::FB_CONFIG_TWO_SUBPASSES);
		}
	} else {
		ERR_FAIL(); 
	}
	p_render_data->scene_data->emissive_exposure_normalization = -1.0;
	RD::get_singleton()->draw_command_begin_label("Render Setup");
	_setup_lightmaps(p_render_data, *p_render_data->lightmaps, p_render_data->scene_data->cam_transform);
	_setup_environment(p_render_data, is_reflection_probe, screen_size, !is_reflection_probe, p_default_bg_color, false);
	_update_render_base_uniform_set(); 
	RD::get_singleton()->draw_command_end_label(); 
	
	RID radiance_texture;
	bool draw_sky = false;
	bool draw_sky_fog_only = false;
	
	float sky_energy_multiplier = 1.0 / _render_buffers_get_luminance_multiplier();
	Color clear_color = p_default_bg_color;
	bool keep_color = false;
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_OVERDRAW) {
		clear_color = Color(0, 0, 0, 1);