### 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)

}
		} else {
			spec_constant_base_flags |= 1 << SPEC_CONSTANT_DISABLE_DIRECTIONAL_LIGHTS;
		}
		if (!is_environment(p_render_data->environment) || !environment_get_fog_enabled(p_render_data->environment)) {
			spec_constant_base_flags |= 1 << SPEC_CONSTANT_DISABLE_FOG;
		}
	}
	{
		if (rb_data.is_valid()) {
			RD::get_singleton()->draw_command_begin_label("Render 3D Pass");
		} else {
			RD::get_singleton()->draw_command_begin_label("Render Reflection Probe Pass");
		}
		
		RD::get_singleton()->draw_command_begin_label("Render Opaque Subpass");
		p_render_data->scene_data->directional_light_count = p_render_data->directional_light_count;
		_setup_environment(p_render_data, is_reflection_probe, screen_size, !is_reflection_probe, p_default_bg_color, p_render_data->render_buffers.is_valid());
		if (using_subpass_transparent && using_subpass_post_process) {
			RENDER_TIMESTAMP("Render Opaque + Transparent + Tonemap");
		} else if (using_subpass_transparent) {
			RENDER_TIMESTAMP("Render Opaque + Transparent");
		} else {
			RENDER_TIMESTAMP("Render Opaque");
		}
		RID rp_uniform_set = _setup_render_pass_uniform_set(RENDER_LIST_OPAQUE, p_render_data, radiance_texture, true);
		bool can_continue_color = !using_subpass_transparent && !scene_state.used_screen_texture;
		bool can_continue_depth = !using_subpass_transparent && !scene_state.used_depth_texture;
		{