### 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)

RID env = is_environment(p_render_data->environment) ? p_render_data->environment : RID();
	RID reflection_probe_instance = p_render_data->reflection_probe.is_valid() ? RendererRD::LightStorage::get_singleton()->reflection_probe_instance_get_probe(p_render_data->reflection_probe) : RID();
	
	if (p_index >= (int)scene_state.uniform_buffers.size()) {
		uint32_t from = scene_state.uniform_buffers.size();
		scene_state.uniform_buffers.resize(p_index + 1);
		for (uint32_t i = from; i < scene_state.uniform_buffers.size(); i++) {
			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);
}
void RenderForwardMobile::_fill_element_info(RenderListType p_render_list, uint32_t p_offset, int32_t p_max_elements) {
	RenderList *rl = &render_list[p_render_list];
	uint32_t element_total = p_max_elements >= 0 ? uint32_t(p_max_elements) : rl->elements.size();
	rl->element_info.resize(p_offset + element_total);
	for (uint32_t i = 0; i < element_total; i++) {
		GeometryInstanceSurfaceDataCache *surface = rl->elements[i + p_offset];
		RenderElementInfo &element_info = rl->element_info[p_offset + i];
		element_info.lod_index = surface->lod_index;
		element_info.uses_lightmap = surface->sort.uses_lightmap;
	}
}
void RenderForwardMobile::_render_list(RenderingDevice::DrawListID p_draw_list, RenderingDevice::FramebufferFormatID p_framebuffer_Format, RenderListParameters *p_params, uint32_t p_from_element, uint32_t p_to_element) {