### 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)
key_array.push_back(flip_v);
					key_array.push_back(transpose);
					Array value_array;
					value_array.push_back(source_id);
					value_array.push_back(coords);
					value_array.push_back(alternative_tile);
					if (!compatibility_tilemap_mapping.has(E.key)) {
						compatibility_tilemap_mapping[E.key] = RBMap<Array, Array>();
					}
					compatibility_tilemap_mapping[E.key][key_array] = value_array;
					compatibility_tilemap_mapping_tile_modes[E.key] = COMPATIBILITY_TILE_MODE_SINGLE_TILE;
					TileData *tile_data = atlas_source->get_tile_data(coords, alternative_tile);
					ERR_CONTINUE(!tile_data);
					tile_data->set_flip_h(flip_h);
					tile_data->set_flip_v(flip_v);
					tile_data->set_transpose(transpose);
					tile_data->set_material(ctd->material);
					tile_data->set_modulate(ctd->modulate);
					tile_data->set_z_index(ctd->z_index);
					if (ctd->occluder.is_valid()) {
						if (get_occlusion_layers_count() < 1) {
							add_occlusion_layer();
						};
						Ref<OccluderPolygon2D> occluder = ctd->occluder->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);