### 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)
break;
			}
			for (unsigned int i = 0; i < polygons.size(); i++) {
				Vector<Point2> new_polygon;
				for (const Vector2 &vec : polygons[i]) {
					Vector2 point = vec;
					switch (p_item_pressed) {
						case ROTATE_RIGHT: {
							point = Vector2(-point.y, point.x);
						} break;
						case ROTATE_LEFT: {
							point = Vector2(point.y, -point.x);
						} break;
						case FLIP_HORIZONTALLY: {
							point = Vector2(-point.x, point.y);
						} break;
						case FLIP_VERTICALLY: {
							point = Vector2(point.x, -point.y);
						} break;
						default:
							break;
					}
					new_polygon.push_back(point);
				}
				undo_redo->add_do_method(this, "set_polygon", i, new_polygon);
			}
			undo_redo->add_do_method(base_control, "queue_redraw");
			undo_redo->add_do_method(this, "emit_signal", "polygons_changed");
			for (unsigned int i = 0; i < polygons.size(); i++) {
				undo_redo->add_undo_method(this, "set_polygon", i, polygons[i]);