### 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)
HashMap<Vector2i, CellData>::ConstIterator E = tile_map.find(p_coords);
	if (!E) {
		return TileSetSource::INVALID_TILE_ALTERNATIVE;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (p_use_proxies && tile_set.is_valid()) {
		Array proxyed = tile_set->map_tile_proxy(E->value.cell.source_id, E->value.cell.get_atlas_coords(), E->value.cell.alternative_tile);
		return proxyed[2];
	}
	return E->value.cell.alternative_tile;
}
TileData *TileMapLayer::get_cell_tile_data(const Vector2i &p_coords, bool p_use_proxies) const {
	int source_id = get_cell_source_id(p_coords, p_use_proxies);
	if (source_id == TileSet::INVALID_SOURCE) {
		return nullptr;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	Ref<TileSetAtlasSource> source = tile_set->get_source(source_id);
	if (source.is_valid()) {
		return source->get_tile_data(get_cell_atlas_coords(p_coords, p_use_proxies), get_cell_alternative_tile(p_coords, p_use_proxies));
	}
	return nullptr;
}
void TileMapLayer::clear() {