### 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)
const TileMapCell &c = r_cell_data.cell;
	TileSetSource *source;
	if (tile_set->has_source(c.source_id)) {
		source = *tile_set->get_source(c.source_id);
		if (source->has_tile(c.get_atlas_coords()) && source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				const TileData *tile_data;
				if (r_cell_data.runtime_tile_data_cache) {
					tile_data = r_cell_data.runtime_tile_data_cache;
				} else {
					tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
				}
				Transform2D cell_to_quadrant;
				cell_to_quadrant.set_origin(tile_map_node->map_to_local(r_cell_data.coords) - p_quadrant_pos);
				rs->canvas_item_add_set_transform(p_canvas_item, cell_to_quadrant);
				for (int layer_index = 0; layer_index < tile_set->get_navigation_layers_count(); layer_index++) {
					Ref<NavigationPolygon> navigation_polygon = tile_data->get_navigation_polygon(layer_index);
					if (navigation_polygon.is_valid()) {
						navigation_polygon = tile_map_node->get_transformed_polygon(Ref<Resource>(navigation_polygon), c.alternative_tile);
						Vector<Vector2> navigation_polygon_vertices = navigation_polygon->get_vertices();
						if (navigation_polygon_vertices.size() < 3) {
							continue;
						}
						for (int i = 0; i < navigation_polygon->get_polygon_count(); i++) {
							
							Vector<int> polygon = navigation_polygon->get_polygon(i);
							Vector<Vector2> debug_polygon_vertices;
							debug_polygon_vertices.resize(polygon.size());
							for (int j = 0; j < polygon.size(); j++) {