### 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)

RD::DrawListID draw_list = RD::get_singleton()->draw_list_switch_to_next_pass();
			sky.draw_sky(draw_list, rb, p_render_data->environment, framebuffer, time, sky_energy_multiplier);
			RD::get_singleton()->draw_command_end_label(); 
			
		} else {
			
			RD::get_singleton()->draw_list_switch_to_next_pass();
		}
		if (!using_subpass_transparent) {
			
			RD::get_singleton()->draw_list_end(RD::BARRIER_MASK_ALL_BARRIERS);
			RD::get_singleton()->draw_command_end_label(); 
		}
		if (scene_state.used_screen_texture) {
			
			_render_buffers_copy_screen_texture(p_render_data);
		}
		if (scene_state.used_depth_texture) {
			
			_render_buffers_copy_depth_texture(p_render_data);
		}
		
		RD::get_singleton()->draw_command_begin_label("Render Transparent Subpass");
		rp_uniform_set = _setup_render_pass_uniform_set(RENDER_LIST_ALPHA, p_render_data, radiance_texture, true);
		if (using_subpass_transparent) {
			RD::FramebufferFormatID fb_format = RD::get_singleton()->framebuffer_get_format(framebuffer);
			RenderListParameters render_list_params(render_list[RENDER_LIST_ALPHA].elements.ptr(), render_list[RENDER_LIST_ALPHA].element_info.ptr(), render_list[RENDER_LIST_ALPHA].elements.size(), reverse_cull, PASS_MODE_COLOR_TRANSPARENT, rp_uniform_set, spec_constant_base_flags, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_WIREFRAME, Vector2(), p_render_data->scene_data->lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, p_render_data->scene_data->view_count);
			render_list_params.framebuffer_format = fb_format;
			if ((uint32_t)render_list_params.element_count > render_list_thread_threshold && false) {