### 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)

dc.set_depth_correction(true);
		Projection cms[RendererSceneRender::MAX_RENDER_VIEWS];
		for (uint32_t v = 0; v < p_render_data->scene_data->view_count; v++) {
			cms[v] = (dc * p_render_data->scene_data->view_projection[v]) * Projection(p_render_data->scene_data->cam_transform.affine_inverse());
		}
		_debug_sdfgi_probes(rb, color_only_framebuffer, p_render_data->scene_data->view_count, cms, will_continue_color, will_continue_depth);
	}
	if (draw_sky || draw_sky_fog_only) {
		RENDER_TIMESTAMP("Render Sky");
		RD::get_singleton()->draw_command_begin_label("Draw Sky");
		RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(color_only_framebuffer, RD::INITIAL_ACTION_CONTINUE, can_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, can_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ);
		sky.draw_sky(draw_list, rb, p_render_data->environment, color_only_framebuffer, time, sky_energy_multiplier);
		RD::get_singleton()->draw_list_end();
		RD::get_singleton()->draw_command_end_label();
	}
	if (rb->get_msaa_3d() != RS::VIEWPORT_MSAA_DISABLED) {
		RENDER_TIMESTAMP("Resolve MSAA");
		if (!can_continue_color) {
			
			for (uint32_t v = 0; v < rb->get_view_count(); v++) {
				RD::get_singleton()->texture_resolve_multisample(rb_data->get_color_msaa(v), rb->get_internal_texture(v));
			}
			if (using_separate_specular) {
				for (uint32_t v = 0; v < rb->get_view_count(); v++) {
					RD::get_singleton()->texture_resolve_multisample(rb_data->get_specular_msaa(v), rb_data->get_specular(v));
				}
			}
		}
		if (!can_continue_depth) {
			for (uint32_t v = 0; v < rb->get_view_count(); v++) {