### 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)
virtual void remove_navigation_layer(int p_index){};
	virtual void add_custom_data_layer(int p_index){};
	virtual void move_custom_data_layer(int p_from_index, int p_to_pos){};
	virtual void remove_custom_data_layer(int p_index){};
	virtual void reset_state() override;
	
	virtual int get_tiles_count() const = 0;
	virtual Vector2i get_tile_id(int tile_index) const = 0;
	virtual bool has_tile(Vector2i p_atlas_coords) const = 0;
	
	virtual int get_alternative_tiles_count(const Vector2i p_atlas_coords) const = 0;
	virtual int get_alternative_tile_id(const Vector2i p_atlas_coords, int p_index) const = 0;
	virtual bool has_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) const = 0;
};
class TileSetAtlasSource : public TileSetSource {
	GDCLASS(TileSetAtlasSource, TileSetSource);
public:
	enum TileAnimationMode {
		TILE_ANIMATION_MODE_DEFAULT,
		TILE_ANIMATION_MODE_RANDOM_START_TIMES,
		TILE_ANIMATION_MODE_MAX,
	};
	enum TransformBits {
		TRANSFORM_FLIP_H = 1 << 12,
		TRANSFORM_FLIP_V = 1 << 13,
		TRANSFORM_TRANSPOSE = 1 << 14,
	};
private:
	struct TileAlternativesData {
		Vector2i size_in_atlas = Vector2i(1, 1);