### 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)
GDCLASS(TileMapPattern, Resource);
	Size2i size;
	HashMap<Vector2i, TileMapCell> pattern;
	void _set_tile_data(const Vector<int> &p_data);
	Vector<int> _get_tile_data() const;
protected:
	bool _set(const StringName &p_name, const Variant &p_value);
	bool _get(const StringName &p_name, Variant &r_ret) const;
	void _get_property_list(List<PropertyInfo> *p_list) const;
	static void _bind_methods();
public:
	void set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile = 0);
	bool has_cell(const Vector2i &p_coords) const;
	void remove_cell(const Vector2i &p_coords, bool p_update_size = true);
	int get_cell_source_id(const Vector2i &p_coords) const;
	Vector2i get_cell_atlas_coords(const Vector2i &p_coords) const;
	int get_cell_alternative_tile(const Vector2i &p_coords) const;
	const HashMap<Vector2i, TileMapCell> &get_pattern() const { return pattern; }
	TypedArray<Vector2i> get_used_cells() const;
	Size2i get_size() const;
	void set_size(const Size2i &p_size);
	bool is_empty() const;
	void clear();
};
class TileSet : public Resource {