### 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)

reflection_probe_count = p_reflection_probe_instance_count < (uint32_t)MAX_RDL_CULL ? p_reflection_probe_instance_count : (uint32_t)MAX_RDL_CULL;
	for (uint32_t i = 0; i < reflection_probe_count; i++) {
		reflection_probes[i] = RendererRD::LightStorage::get_singleton()->reflection_probe_instance_get_forward_id(p_reflection_probe_instances[i]);
	}
}
void RenderForwardMobile::GeometryInstanceForwardMobile::pair_decal_instances(const RID *p_decal_instances, uint32_t p_decal_instance_count) {
	decals_count = p_decal_instance_count < (uint32_t)MAX_RDL_CULL ? p_decal_instance_count : (uint32_t)MAX_RDL_CULL;
	for (uint32_t i = 0; i < decals_count; i++) {
		decals[i] = RendererRD::TextureStorage::get_singleton()->decal_instance_get_forward_id(p_decal_instances[i]);
	}
}
void RenderForwardMobile::GeometryInstanceForwardMobile::set_softshadow_projector_pairing(bool p_softshadow, bool p_projector) {
	use_projector = p_projector;
	use_soft_shadow = p_softshadow;
}
void RenderForwardMobile::GeometryInstanceForwardMobile::_mark_dirty() {
	if (dirty_list_element.in_list()) {
		return;
	}
	
	GeometryInstanceSurfaceDataCache *surf = surface_caches;
	while (surf) {
		GeometryInstanceSurfaceDataCache *next = surf->next;
		RenderForwardMobile::get_singleton()->geometry_instance_surface_alloc.free(surf);
		surf = next;
	}
	surface_caches = nullptr;
	RenderForwardMobile::get_singleton()->geometry_instance_dirty_list.add(&dirty_list_element);
}
void RenderForwardMobile::_geometry_instance_add_surface_with_material(GeometryInstanceForwardMobile *ginstance, uint32_t p_surface, SceneShaderForwardMobile::MaterialData *p_material, uint32_t p_material_id, uint32_t p_shader_id, RID p_mesh) {