### 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)
points.push_back(Vector2(-0.5, 0.0));
		points.push_back(Vector2(0.0, 0.5));
		points.push_back(Vector2(0.5, 0.0));
	} else {
		float overlap = 0.0;
		switch (tile_shape) {
			case TileSet::TILE_SHAPE_HEXAGON:
				overlap = 0.25;
				break;
			case TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE:
				overlap = 0.0;
				break;
			default:
				break;
		}
		points.push_back(Vector2(0.0, -0.5));
		points.push_back(Vector2(-0.5, overlap - 0.5));
		points.push_back(Vector2(-0.5, 0.5 - overlap));
		points.push_back(Vector2(0.0, 0.5));
		points.push_back(Vector2(0.5, 0.5 - overlap));
		points.push_back(Vector2(0.5, overlap - 0.5));
		if (get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL) {
			for (int i = 0; i < points.size(); i++) {
				points.write[i] = Vector2(points[i].y, points[i].x);
			}
		}
	}
	return points;
}
void TileSet::draw_tile_shape(CanvasItem *p_canvas_item, Transform2D p_transform, Color p_color, bool p_filled, Ref<Texture2D> p_texture) {