### 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)
const Vector2 *r = p_vertices.ptr();
	int size = p_vertices.size();
	PackedVector2Array new_points;
	new_points.resize(size);
	Vector2 *w = new_points.ptrw();
	bool flip_h = (p_alternative_id & TileSetAtlasSource::TRANSFORM_FLIP_H);
	bool flip_v = (p_alternative_id & TileSetAtlasSource::TRANSFORM_FLIP_V);
	bool transpose = (p_alternative_id & TileSetAtlasSource::TRANSFORM_TRANSPOSE);
	for (int i = 0; i < size; i++) {
		Vector2 v;
		if (transpose) {
			v = Vector2(r[i].y, r[i].x);
		} else {
			v = r[i];
		}
		if (flip_h) {
			v.x *= -1;
		}
		if (flip_v) {
			v.y *= -1;
		}
		w[i] = v;
	}
	return new_points;
}
bool TileMap::_set(const StringName &p_name, const Variant &p_value) {