### 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)
Vector<Vector2> point_list = {
		Vector2(3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(0, 3),
		Vector2(-3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-3, -3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(0, -3),
		Vector2(3, -3.0 * (1.0 - p_overlap * 2.0))
	};
	Vector2 unit = Vector2(p_size) / 6.0;
	Vector<Vector2> polygon;
	if (p_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		for (int i = 0; i < point_list.size(); i++) {
			point_list.write[i] = point_list[i] * unit;
		}
		switch (p_bit) {
			case TileSet::CELL_NEIGHBOR_RIGHT_SIDE:
				polygon.push_back(point_list[5]);
				polygon.push_back(point_list[0]);
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE:
				polygon.push_back(point_list[0]);
				polygon.push_back(point_list[1]);