### 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)

scene_state.uniform_buffers[i] = p_render_data->scene_data->create_uniform_buffer();
		}
	}
	p_render_data->scene_data->update_ubo(scene_state.uniform_buffers[p_index], get_debug_draw_mode(), env, reflection_probe_instance, p_render_data->camera_attributes, p_flip_y, p_pancake_shadows, p_screen_size, p_default_bg_color, _render_buffers_get_luminance_multiplier(), p_opaque_render_buffers);
	
	scene_state.ubo.cluster_shift = get_shift_from_power_of_2(p_render_data->cluster_size);
	scene_state.ubo.max_cluster_element_count_div_32 = p_render_data->cluster_max_elements / 32;
	{
		uint32_t cluster_screen_width = (p_screen_size.width - 1) / p_render_data->cluster_size + 1;
		uint32_t cluster_screen_height = (p_screen_size.height - 1) / p_render_data->cluster_size + 1;
		scene_state.ubo.cluster_type_size = cluster_screen_width * cluster_screen_height * (scene_state.ubo.max_cluster_element_count_div_32 + 32);
		scene_state.ubo.cluster_width = cluster_screen_width;
	}
	scene_state.ubo.gi_upscale_for_msaa = false;
	scene_state.ubo.volumetric_fog_enabled = false;
	if (rd.is_valid()) {
		if (rd->get_msaa_3d() != RS::VIEWPORT_MSAA_DISABLED) {
			scene_state.ubo.gi_upscale_for_msaa = true;
		}
		if (rd->has_custom_data(RB_SCOPE_FOG)) {
			Ref<RendererRD::Fog::VolumetricFog> fog = rd->get_custom_data(RB_SCOPE_FOG);
			scene_state.ubo.volumetric_fog_enabled = true;
			float fog_end = fog->length;
			if (fog_end > 0.0) {
				scene_state.ubo.volumetric_fog_inv_length = 1.0 / fog_end;
			} else {
				scene_state.ubo.volumetric_fog_inv_length = 1.0;
			}
			float fog_detail_spread = fog->spread; 
			if (fog_detail_spread > 0.0) {