### 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)

shader_version = SceneShaderForwardMobile::SHADER_VERSION_SHADOW_PASS_DP;
			} break;
			case PASS_MODE_DEPTH_MATERIAL: {
				ERR_FAIL_COND_MSG(p_params->view_count > 1, "Multiview not supported for material pass");
				shader_version = SceneShaderForwardMobile::SHADER_VERSION_DEPTH_PASS_WITH_MATERIAL;
			} break;
		}
		PipelineCacheRD *pipeline = nullptr;
		pipeline = &shader->pipelines[cull_variant][primitive][shader_version];
		RD::VertexFormatID vertex_format = -1;
		RID vertex_array_rd;
		RID index_array_rd;
		
		if (surf->owner->mesh_instance.is_valid()) {
			mesh_storage->mesh_instance_surface_get_vertex_arrays_and_format(surf->owner->mesh_instance, surf->surface_index, pipeline->get_vertex_input_mask(), vertex_array_rd, vertex_format);
		} else {
			mesh_storage->mesh_surface_get_vertex_arrays_and_format(mesh_surface, pipeline->get_vertex_input_mask(), vertex_array_rd, vertex_format);
		}
		index_array_rd = mesh_storage->mesh_surface_get_index_array(mesh_surface, element_info.lod_index);
		if (prev_vertex_array_rd != vertex_array_rd) {
			RD::get_singleton()->draw_list_bind_vertex_array(draw_list, vertex_array_rd);
			prev_vertex_array_rd = vertex_array_rd;
		}
		if (prev_index_array_rd != index_array_rd) {
			if (index_array_rd.is_valid()) {
				RD::get_singleton()->draw_list_bind_index_array(draw_list, index_array_rd);
			}
			prev_index_array_rd = index_array_rd;
		}
		RID pipeline_rd = pipeline->get_render_pipeline(vertex_format, framebuffer_format, p_params->force_wireframe, p_params->subpass, base_spec_constants);