### 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 set_use_parent_material(bool p_use_parent_material) override;
	virtual void set_texture_filter(CanvasItem::TextureFilter p_texture_filter) override;
	virtual void set_texture_repeat(CanvasItem::TextureRepeat p_texture_repeat) override;
	
	Vector2i get_coords_for_body_rid(RID p_physics_body);
	
	int get_layer_for_body_rid(RID p_physics_body);
	
	void fix_invalid_tiles();
	
	void clear_layer(int p_layer);
	void clear();
	
	void update_internals();
	void notify_runtime_tile_data_update(int p_layer = -1);
	
	TypedArray<Vector2i> get_surrounding_cells(const Vector2i &coords);
	void draw_cells_outline(Control *p_control, const RBSet<Vector2i> &p_cells, Color p_color, Transform2D p_transform = Transform2D());
	Ref<Resource> get_transformed_polygon(Ref<Resource> p_polygon, int p_alternative_id);
	
	GDVIRTUAL2R(bool, _use_tile_data_runtime_update, int, Vector2i);
	GDVIRTUAL3(_tile_data_runtime_update, int, Vector2i, TileData *);
	
	PackedStringArray get_configuration_warnings() const override;
	TileMap();
	~TileMap();
};
VARIANT_ENUM_CAST(TileMap::VisibilityMode);
#endif