### 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)
tile_data->set_modulate(ctd->modulate);
							tile_data->set_z_index(ctd->z_index);
							if (ctd->autotile_occluder_map.has(coords)) {
								if (get_occlusion_layers_count() < 1) {
									add_occlusion_layer();
								}
								Ref<OccluderPolygon2D> occluder = ctd->autotile_occluder_map[coords]->duplicate();
								Vector<Vector2> polygon = ctd->occluder->get_polygon();
								for (int index = 0; index < polygon.size(); index++) {
									polygon.write[index] = xform.xform(polygon[index] - ctd->region.get_size() / 2.0);
								}
								occluder->set_polygon(polygon);
								tile_data->set_occluder(0, occluder);
							}
							if (ctd->autotile_navpoly_map.has(coords)) {
								if (get_navigation_layers_count() < 1) {
									add_navigation_layer();
								}
								Ref<NavigationPolygon> navigation = ctd->autotile_navpoly_map[coords]->duplicate();
								Vector<Vector2> vertices = navigation->get_vertices();
								for (int index = 0; index < vertices.size(); index++) {
									vertices.write[index] = xform.xform(vertices[index] - ctd->region.get_size() / 2.0);
								}
								navigation->set_vertices(vertices);
								tile_data->set_navigation_polygon(0, navigation);
							}
							if (ctd->autotile_priority_map.has(coords)) {
								tile_data->set_probability(ctd->autotile_priority_map[coords]);
							}
							if (ctd->autotile_z_index_map.has(coords)) {