### 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)
void _physics_notify_tilemap_change(DirtyFlags p_what);
	void _physics_clear_cell(CellData &r_cell_data);
	void _physics_update_cell(CellData &r_cell_data);
#ifdef DEBUG_ENABLED
	void _physics_draw_cell_debug(const RID &p_canvas_item, const Vector2i &p_quadrant_pos, const CellData &r_cell_data);
#endif 
	bool _navigation_was_cleaned_up = false;
	void _navigation_update();
	void _navigation_clear_cell(CellData &r_cell_data);
	void _navigation_update_cell(CellData &r_cell_data);
#ifdef DEBUG_ENABLED
	void _navigation_draw_cell_debug(const RID &p_canvas_item, const Vector2i &p_quadrant_pos, const CellData &r_cell_data);
#endif 
	bool _scenes_was_cleaned_up = false;
	void _scenes_update();
	void _scenes_clear_cell(CellData &r_cell_data);
	void _scenes_update_cell(CellData &r_cell_data);
#ifdef DEBUG_ENABLED
	void _scenes_draw_cell_debug(const RID &p_canvas_item, const Vector2i &p_quadrant_pos, const CellData &r_cell_data);
#endif 
	
	TileSet::TerrainsPattern _get_best_terrain_pattern_for_constraints(int p_terrain_set, const Vector2i &p_position, const RBSet<TerrainConstraint> &p_constraints, TileSet::TerrainsPattern p_current_pattern);
	RBSet<TerrainConstraint> _get_terrain_constraints_from_added_pattern(const Vector2i &p_position, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern) const;
	RBSet<TerrainConstraint> _get_terrain_constraints_from_painted_cells_list(const RBSet<Vector2i> &p_painted, int p_terrain_set, bool p_ignore_empty_terrains) const;
public:
	
	void set_tile_map(TileMap *p_tile_map);
	void set_layer_index_in_tile_map_node(int p_index);
	
	Rect2 get_rect(bool &r_changed) const;