### 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)
int autotile_spacing = 0;
		HashMap<Vector2i, int> autotile_bitmask_flags;
		HashMap<Vector2i, Ref<OccluderPolygon2D>> autotile_occluder_map;
		HashMap<Vector2i, Ref<NavigationPolygon>> autotile_navpoly_map;
		HashMap<Vector2i, int> autotile_priority_map;
		HashMap<Vector2i, int> autotile_z_index_map;
		Vector<CompatibilityShapeData> shapes;
		Ref<OccluderPolygon2D> occluder;
		Vector2 occluder_offset;
		Ref<NavigationPolygon> navigation;
		Vector2 navigation_offset;
		int z_index = 0;
	};
	enum CompatibilityTileMode {
		COMPATIBILITY_TILE_MODE_SINGLE_TILE = 0,
		COMPATIBILITY_TILE_MODE_AUTO_TILE,
		COMPATIBILITY_TILE_MODE_ATLAS_TILE,
	};
	HashMap<int, CompatibilityTileData *> compatibility_data;
	HashMap<int, int> compatibility_tilemap_mapping_tile_modes;
	HashMap<int, RBMap<Array, Array>> compatibility_tilemap_mapping;
	HashMap<Vector2i, int> compatibility_size_count;
	void _compatibility_conversion();
public:
	
	Array compatibility_tilemap_map(int p_tile_id, Vector2i p_coords, bool p_flip_h, bool p_flip_v, bool p_transpose);
#endif 
public:
	static const int INVALID_SOURCE; 
	enum CellNeighbor {