### 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)

p_render_data->environment = RID(); 
		}
		reverse_cull = true; 
	} else {
		screen_size = rb->get_internal_size();
		if (rb->get_use_taa() || get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_MOTION_VECTORS) {
			color_pass_flags |= COLOR_PASS_FLAG_MOTION_VECTORS;
		}
		if (p_render_data->voxel_gi_instances->size() > 0) {
			using_voxelgi = true;
		}
		if (p_render_data->environment.is_valid()) {
			if (environment_get_sdfgi_enabled(p_render_data->environment)) {
				using_sdfgi = true;
			}
			if (environment_get_ssr_enabled(p_render_data->environment)) {
				using_separate_specular = true;
				using_ssr = true;
				color_pass_flags |= COLOR_PASS_FLAG_SEPARATE_SPECULAR;
			}
		}
		if (p_render_data->scene_data->view_count > 1) {
			color_pass_flags |= COLOR_PASS_FLAG_MULTIVIEW;
		}
		color_framebuffer = rb_data->get_color_pass_fb(color_pass_flags);
		color_only_framebuffer = rb_data->get_color_only_fb();
	}
	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);