### 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 (!tile_map.has(p_coords)) {
		return TileMapCell();
	} else {
		TileMapCell c = tile_map.find(p_coords)->value.cell;
		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(c.source_id, c.get_atlas_coords(), c.alternative_tile);
			c.source_id = proxyed[0];
			c.set_atlas_coords(proxyed[1]);
			c.alternative_tile = proxyed[2];
		}
		return c;
	}
}
void TileMapLayer::set_tile_data(TileMapLayer::DataFormat p_format, const Vector<int> &p_data) {