### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
hovered_segment_index = -1;
	hovered_segment_point = Vector2();
	Transform2D xform;
	xform.set_origin(base_control->get_size() / 2 + panning);
	xform.set_scale(Vector2(editor_zoom_widget->get_zoom(), editor_zoom_widget->get_zoom()));
	Ref<InputEventMouseMotion> mm = p_event;
	if (mm.is_valid()) {
		if (drag_type == DRAG_TYPE_DRAG_POINT) {
			ERR_FAIL_INDEX(drag_polygon_index, (int)polygons.size());
			ERR_FAIL_INDEX(drag_point_index, polygons[drag_polygon_index].size());
			Point2 point = xform.affine_inverse().xform(mm->get_position());
			float distance = grab_threshold * 2.0;
			_snap_to_tile_shape(point, distance, grab_threshold / editor_zoom_widget->get_zoom());
			_snap_point(point);
			polygons[drag_polygon_index].write[drag_point_index] = point;
		} else if (drag_type == DRAG_TYPE_PAN) {
			panning += mm->get_position() - drag_last_pos;
			drag_last_pos = mm->get_position();
			button_center_view->set_disabled(panning.is_zero_approx());
		} else {
			
			_grab_polygon_point(mm->get_position(), xform, hovered_polygon_index, hovered_point_index);
			
			if (hovered_point_index == -1) {
				_grab_polygon_segment_point(mm->get_position(), xform, hovered_polygon_index, hovered_segment_index, hovered_segment_point);
			}
		}
	}
	Ref<InputEventMouseButton> mb = p_event;
	if (mb.is_valid()) {