### 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<int, Ref<TileSetSource>> sources;
	Vector<int> source_ids;
	int next_source_id = 0;
	
	LocalVector<Ref<TileMapPattern>> patterns;
	void _compute_next_source_id();
	void _source_changed();
	
	RBMap<int, int> source_level_proxies;
	RBMap<Array, Array> coords_level_proxies;
	RBMap<Array, Array> alternative_level_proxies;
	
	Vector<Point2> _get_square_terrain_polygon(Vector2i p_size);
	Vector<Point2> _get_square_corner_or_side_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_square_corner_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_square_side_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_isometric_terrain_polygon(Vector2i p_size);
	Vector<Point2> _get_isometric_corner_or_side_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_isometric_corner_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_isometric_side_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_half_offset_terrain_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis);
	Vector<Point2> _get_half_offset_corner_or_side_terrain_peering_bit_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_half_offset_corner_terrain_peering_bit_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis, TileSet::CellNeighbor p_bit);
	Vector<Point2> _get_half_offset_side_terrain_peering_bit_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis, TileSet::CellNeighbor p_bit);
protected:
	static void _bind_methods();
public:
	
	Vector<TileSetPlugin *> get_tile_set_atlas_plugins() const;