### 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)
for (int i = 0; i < scenes_ids.size(); i++) {
		p_list->push_back(PropertyInfo(Variant::OBJECT, vformat("%s/%d/%s", PNAME("scenes"), scenes_ids[i], PNAME("scene")), PROPERTY_HINT_RESOURCE_TYPE, "TileSetScenesCollectionSource"));
		PropertyInfo property_info = PropertyInfo(Variant::BOOL, vformat("%s/%d/%s", PNAME("scenes"), scenes_ids[i], PNAME("display_placeholder")));
		if (scenes[scenes_ids[i]].display_placeholder == false) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		p_list->push_back(property_info);
	}
}
void TileSetScenesCollectionSource::_bind_methods() {
	ClassDB::bind_method(D_METHOD("get_scene_tiles_count"), &TileSetScenesCollectionSource::get_scene_tiles_count);
	ClassDB::bind_method(D_METHOD("get_scene_tile_id", "index"), &TileSetScenesCollectionSource::get_scene_tile_id);
	ClassDB::bind_method(D_METHOD("has_scene_tile_id", "id"), &TileSetScenesCollectionSource::has_scene_tile_id);
	ClassDB::bind_method(D_METHOD("create_scene_tile", "packed_scene", "id_override"), &TileSetScenesCollectionSource::create_scene_tile, DEFVAL(INVALID_TILE_ALTERNATIVE));
	ClassDB::bind_method(D_METHOD("set_scene_tile_id", "id", "new_id"), &TileSetScenesCollectionSource::set_scene_tile_id);
	ClassDB::bind_method(D_METHOD("set_scene_tile_scene", "id", "packed_scene"), &TileSetScenesCollectionSource::set_scene_tile_scene);
	ClassDB::bind_method(D_METHOD("get_scene_tile_scene", "id"), &TileSetScenesCollectionSource::get_scene_tile_scene);
	ClassDB::bind_method(D_METHOD("set_scene_tile_display_placeholder", "id", "display_placeholder"), &TileSetScenesCollectionSource::set_scene_tile_display_placeholder);
	ClassDB::bind_method(D_METHOD("get_scene_tile_display_placeholder", "id"), &TileSetScenesCollectionSource::get_scene_tile_display_placeholder);
	ClassDB::bind_method(D_METHOD("remove_scene_tile", "id"), &TileSetScenesCollectionSource::remove_scene_tile);
	ClassDB::bind_method(D_METHOD("get_next_scene_tile_id"), &TileSetScenesCollectionSource::get_next_scene_tile_id);
}
void TileData::set_tile_set(const TileSet *p_tile_set) {
	tile_set = p_tile_set;
	notify_tile_data_properties_should_change();
}
void TileData::notify_tile_data_properties_should_change() {