### 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)
return Vector2i(coord_x, coord_y);
	}
	void set_atlas_coords(const Vector2i &r_coords) {
		coord_x = r_coords.x;
		coord_y = r_coords.y;
	}
	bool operator<(const TileMapCell &p_other) const {
		if (source_id == p_other.source_id) {
			if (coord_x == p_other.coord_x) {
				if (coord_y == p_other.coord_y) {
					return alternative_tile < p_other.alternative_tile;
				} else {
					return coord_y < p_other.coord_y;
				}
			} else {
				return coord_x < p_other.coord_x;
			}
		} else {
			return source_id < p_other.source_id;
		}
	}
	bool operator!=(const TileMapCell &p_other) const {
		return !(source_id == p_other.source_id && coord_x == p_other.coord_x && coord_y == p_other.coord_y && alternative_tile == p_other.alternative_tile);
	}
	bool operator==(const TileMapCell &p_other) const {
		return source_id == p_other.source_id && coord_x == p_other.coord_x && coord_y == p_other.coord_y && alternative_tile == p_other.alternative_tile;
	}
};
class TileMapPattern : public Resource {