### 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)

}
				if (p_color_pass_flags & COLOR_PASS_FLAG_MOTION_VECTORS) {
					if ((flags & (INSTANCE_DATA_FLAG_MULTIMESH | INSTANCE_DATA_FLAG_PARTICLES)) == INSTANCE_DATA_FLAG_MULTIMESH && RendererRD::MeshStorage::get_singleton()->_multimesh_enable_motion_vectors(inst->data->base)) {
						inst->transforms_uniform_set = mesh_storage->multimesh_get_3d_uniform_set(inst->data->base, scene_shader.default_shader_rd, TRANSFORMS_UNIFORM_SET);
					}
				}
			} else if (p_pass_mode == PASS_MODE_SHADOW || p_pass_mode == PASS_MODE_SHADOW_DP) {
				if (surf->flags & GeometryInstanceSurfaceDataCache::FLAG_PASS_SHADOW) {
					rl->add_element(surf);
				}
			} else {
				if (surf->flags & (GeometryInstanceSurfaceDataCache::FLAG_PASS_DEPTH | GeometryInstanceSurfaceDataCache::FLAG_PASS_OPAQUE)) {
					rl->add_element(surf);
				}
			}
			surf->sort.depth_layer = depth_layer;
			surf = surf->next;
		}
	}
	if (p_render_list == RENDER_LIST_OPAQUE && lightmap_captures_used) {
		RD::get_singleton()->buffer_update(scene_state.lightmap_capture_buffer, 0, sizeof(LightmapCaptureData) * lightmap_captures_used, scene_state.lightmap_captures, RD::BARRIER_MASK_RASTER);
	}
}
void RenderForwardClustered::_setup_voxelgis(const PagedArray<RID> &p_voxelgis) {
	scene_state.voxelgis_used = MIN(p_voxelgis.size(), uint32_t(MAX_VOXEL_GI_INSTANCESS));
	for (uint32_t i = 0; i < scene_state.voxelgis_used; i++) {
		scene_state.voxelgi_ids[i] = p_voxelgis[i];
	}
}
void RenderForwardClustered::_setup_lightmaps(const RenderDataRD *p_render_data, const PagedArray<RID> &p_lightmaps, const Transform3D &p_cam_transform) {