### 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)
polygon_editor->set_tile_set(tile_set);
}
void TileDataNavigationEditor::_notification(int p_what) {
	switch (p_what) {
		case NOTIFICATION_ENTER_TREE: {
#ifdef DEBUG_ENABLED
			polygon_editor->set_polygons_color(NavigationServer2D::get_singleton()->get_debug_navigation_geometry_face_color());
#endif 
		} break;
	}
}
TileDataNavigationEditor::TileDataNavigationEditor() {
	polygon_editor = memnew(GenericTilePolygonEditor);
	polygon_editor->set_multiple_polygon_mode(true);
	add_child(polygon_editor);
}
void TileDataNavigationEditor::draw_over_tile(CanvasItem *p_canvas_item, Transform2D p_transform, TileMapCell p_cell, bool p_selected) {
	TileData *tile_data = _get_tile_data(p_cell);
	ERR_FAIL_NULL(tile_data);
	
	RenderingServer::get_singleton()->canvas_item_add_set_transform(p_canvas_item->get_canvas_item(), p_transform);
	Ref<NavigationPolygon> nav_polygon = tile_data->get_navigation_polygon(navigation_layer);
	if (nav_polygon.is_valid()) {
		Vector<Vector2> verts = nav_polygon->get_vertices();
		if (verts.size() < 3) {
			return;
		}
		Color color = Color(0.5, 1.0, 1.0, 1.0);
#ifdef DEBUG_ENABLED