### 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)

RendererRD::MeshStorage *mesh_storage = RendererRD::MeshStorage::get_singleton();
	bool has_read_screen_alpha = p_material->shader_data->uses_screen_texture || p_material->shader_data->uses_depth_texture || p_material->shader_data->uses_normal_texture;
	bool has_base_alpha = (p_material->shader_data->uses_alpha && (!p_material->shader_data->uses_alpha_clip || p_material->shader_data->uses_alpha_antialiasing)) || has_read_screen_alpha;
	bool has_blend_alpha = p_material->shader_data->uses_blend_alpha;
	bool has_alpha = has_base_alpha || has_blend_alpha;
	uint32_t flags = 0;
	if (p_material->shader_data->uses_sss) {
		flags |= GeometryInstanceSurfaceDataCache::FLAG_USES_SUBSURFACE_SCATTERING;
	}
	if (p_material->shader_data->uses_screen_texture) {
		flags |= GeometryInstanceSurfaceDataCache::FLAG_USES_SCREEN_TEXTURE;
	}
	if (p_material->shader_data->uses_depth_texture) {
		flags |= GeometryInstanceSurfaceDataCache::FLAG_USES_DEPTH_TEXTURE;
	}
	if (p_material->shader_data->uses_normal_texture) {
		flags |= GeometryInstanceSurfaceDataCache::FLAG_USES_NORMAL_TEXTURE;
	}
	if (ginstance->data->cast_double_sided_shadows) {
		flags |= GeometryInstanceSurfaceDataCache::FLAG_USES_DOUBLE_SIDED_SHADOWS;