### 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)

Vector<Color> c;
			c.push_back(clear_color.srgb_to_linear()); 
			if (rb_data.is_valid()) {
				if (p_render_data->render_buffers->get_msaa_3d() != RS::VIEWPORT_MSAA_DISABLED) {
					c.push_back(clear_color.srgb_to_linear()); 
				}
				if (using_subpass_post_process) {
					c.push_back(Color()); 
				}
			}
			RD::FramebufferFormatID fb_format = RD::get_singleton()->framebuffer_get_format(framebuffer);
			RenderListParameters render_list_params(render_list[RENDER_LIST_OPAQUE].elements.ptr(), render_list[RENDER_LIST_OPAQUE].element_info.ptr(), render_list[RENDER_LIST_OPAQUE].elements.size(), reverse_cull, PASS_MODE_COLOR, 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) {
				
				
				thread_draw_lists.resize(WorkerThreadPool::get_singleton()->get_thread_count());
				RD::get_singleton()->draw_list_begin_split(framebuffer, thread_draw_lists.size(), thread_draw_lists.ptr(), keep_color ? RD::INITIAL_ACTION_KEEP : RD::INITIAL_ACTION_CLEAR, can_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CLEAR, can_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, c, 1.0, 0);
				WorkerThreadPool::GroupID group_task = WorkerThreadPool::get_singleton()->add_template_group_task(this, &RenderForwardMobile::_render_list_thread_function, &render_list_params, thread_draw_lists.size(), -1, true, SNAME("ForwardMobileRenderList"));
				WorkerThreadPool::get_singleton()->wait_for_group_task_completion(group_task);
			} else {
				
				RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(framebuffer, keep_color ? RD::INITIAL_ACTION_KEEP : RD::INITIAL_ACTION_CLEAR, can_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CLEAR, can_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, c, 1.0, 0);
				_render_list(draw_list, fb_format, &render_list_params, 0, render_list_params.element_count);
			}
		}
		RD::get_singleton()->draw_command_end_label(); 
		if (draw_sky || draw_sky_fog_only) {
			RD::get_singleton()->draw_command_begin_label("Draw Sky Subpass");