### 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)
double picked = Math::random(0.0, sum);
	
	for (const TileMapCell &E : set) {
		if (E.source_id >= 0) {
			Ref<TileSetSource> source = sources[E.source_id];
			Ref<TileSetAtlasSource> atlas_source = source;
			if (atlas_source.is_valid()) {
				TileData *tile_data = atlas_source->get_tile_data(E.get_atlas_coords(), E.alternative_tile);
				count += tile_data->get_probability();
			} else {
				count += 1.0;
			}
		} else {
			count += 1.0;
		}
		if (count >= picked) {
			return E;
		}
	}
	ERR_FAIL_V(TileMapCell());
}
Vector<Vector2> TileSet::get_tile_shape_polygon() {
	Vector<Vector2> points;
	if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		points.push_back(Vector2(-0.5, -0.5));
		points.push_back(Vector2(0.5, -0.5));
		points.push_back(Vector2(0.5, 0.5));
		points.push_back(Vector2(-0.5, 0.5));
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		points.push_back(Vector2(0.0, -0.5));