### 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)

uint32_t surface_count;
				materials = mesh_storage->mesh_get_surface_count_and_materials(mesh, surface_count);
				if (materials) {
					for (uint32_t j = 0; j < surface_count; j++) {
						_geometry_instance_add_surface(ginstance, j, materials[j], mesh);
					}
				}
				ginstance->instance_count = mesh_storage->multimesh_get_instances_to_draw(ginstance->data->base);
			}
		} break;
#if 0
		case RS::INSTANCE_IMMEDIATE: {
			RasterizerStorageGLES3::Immediate *immediate = storage->immediate_owner.get_or_null(inst->base);
			ERR_CONTINUE(!immediate);
			_add_geometry(immediate, inst, nullptr, -1, p_depth_pass, p_shadow_pass);
		} break;
#endif
		case RS::INSTANCE_PARTICLES: {
			int draw_passes = particles_storage->particles_get_draw_passes(ginstance->data->base);
			for (int j = 0; j < draw_passes; j++) {
				RID mesh = particles_storage->particles_get_draw_pass_mesh(ginstance->data->base, j);
				if (!mesh.is_valid()) {
					continue;
				}
				const RID *materials = nullptr;
				uint32_t surface_count;
				materials = mesh_storage->mesh_get_surface_count_and_materials(mesh, surface_count);
				if (materials) {
					for (uint32_t k = 0; k < surface_count; k++) {
						_geometry_instance_add_surface(ginstance, k, materials[k], mesh);