### Godot version

4.1 Beta 3

### System information

Win 10, RTX 2070 mobile

### Issue description

If you set a body to be Top Level using the check box in inspector and save your project, next time you open the project that checkbox is unchecked. Looks like 'project save' somehow ignores that property and doesn't save it,

### Steps to reproduce

1. start a new 3d scene
2. add a 3d node, say, a static body
3. set the node to Top Level by checking the Top Level box in the inspector with the node selected.
4. Save your project
5. Reload project (not scene, project)
6. The box is unchecked

### Minimal reproduction project

n/a
ERR_FAIL_COND_V(!is_inside_tree(), Transform3D());
	/* Due to how threads work at scene level, while this global transform won't be able to be changed from outside a thread,
	 * it is possible that multiple threads can access it while it's dirty from previous work. Due to this, we must ensure that
	 * the dirty/update process is thread safe by utilizing atomic copies.
	 */
	uint32_t dirty = _read_dirty_mask();
	if (dirty & DIRTY_GLOBAL_TRANSFORM) {
		if (dirty & DIRTY_LOCAL_TRANSFORM) {
			_update_local_transform(); 
		}
		Transform3D new_global;
		if (data.parent && !data.top_level) {
			new_global = data.parent->get_global_transform() * data.local_transform;
		} else {
			new_global = data.local_transform;
		}
		if (data.disable_scale) {
			new_global.basis.orthonormalize();
		}
		data.global_transform = new_global;
		_clear_dirty_bits(DIRTY_GLOBAL_TRANSFORM);
	}
	return data.global_transform;
}
#ifdef TOOLS_ENABLED
Transform3D Node3D::get_global_gizmo_transform() const {