### 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)
if (p_tileset == tile_set) {
		return;
	}
	
	if (tile_set.is_valid()) {
		tile_set->disconnect_changed(callable_mp(this, &TileMap::_tile_set_changed));
	}
	tile_set = p_tileset;
	if (tile_set.is_valid()) {
		tile_set->connect_changed(callable_mp(this, &TileMap::_tile_set_changed));
	}
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_TILE_SET);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
}
Ref<TileSet> TileMap::get_tileset() const {