### 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)

_setup_voxelgis(*p_render_data->voxel_gi_instances);
	_setup_environment(p_render_data, is_reflection_probe, screen_size, !is_reflection_probe, p_default_bg_color, false);
	_update_render_base_uniform_set(); 
	_fill_render_list(RENDER_LIST_OPAQUE, p_render_data, PASS_MODE_COLOR, color_pass_flags, using_sdfgi, using_sdfgi || using_voxelgi);
	render_list[RENDER_LIST_OPAQUE].sort_by_key();
	render_list[RENDER_LIST_ALPHA].sort_by_reverse_depth_and_priority();
	_fill_instance_data(RENDER_LIST_OPAQUE, p_render_data->render_info ? p_render_data->render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_VISIBLE] : (int *)nullptr);
	_fill_instance_data(RENDER_LIST_ALPHA);
	RD::get_singleton()->draw_command_end_label();
	if (!is_reflection_probe) {
		if (using_voxelgi) {
			depth_pass_mode = PASS_MODE_DEPTH_NORMAL_ROUGHNESS_VOXEL_GI;
		} else if (p_render_data->environment.is_valid()) {
			if (environment_get_ssr_enabled(p_render_data->environment) ||
					environment_get_sdfgi_enabled(p_render_data->environment) ||
					environment_get_ssao_enabled(p_render_data->environment) ||
					using_ssil ||
					get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_NORMAL_BUFFER ||
					scene_state.used_normal_texture) {
				depth_pass_mode = PASS_MODE_DEPTH_NORMAL_ROUGHNESS;
			}
		} else if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_NORMAL_BUFFER || scene_state.used_normal_texture) {
			depth_pass_mode = PASS_MODE_DEPTH_NORMAL_ROUGHNESS;
		}
		switch (depth_pass_mode) {
			case PASS_MODE_DEPTH: {
				depth_framebuffer = rb_data->get_depth_fb();
			} break;
			case PASS_MODE_DEPTH_NORMAL_ROUGHNESS: {
				depth_framebuffer = rb_data->get_depth_fb(RenderBufferDataForwardClustered::DEPTH_FB_ROUGHNESS);