### 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)
DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_RIGHT_SIDE, 4, 5);
			} else {
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 3, 4);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_SIDE, 4, 5);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_SIDE, 1, 2);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 2, 3);
			}
		}
	}
#undef DRAW_SIDE_IF_NEEDED
}
Ref<Resource> TileMap::get_transformed_polygon(Ref<Resource> p_polygon, int p_alternative_id) {
	if (!bool(p_alternative_id & (TileSetAtlasSource::TRANSFORM_FLIP_H | TileSetAtlasSource::TRANSFORM_FLIP_V | TileSetAtlasSource::TRANSFORM_TRANSPOSE))) {
		return p_polygon;
	}
	{
		HashMap<Pair<Ref<Resource>, int>, Ref<Resource>, PairHash<Ref<Resource>, int>>::Iterator E = polygon_cache.find(Pair<Ref<Resource>, int>(p_polygon, p_alternative_id));
		if (E) {
			return E->value;
		}
	}
	Ref<ConvexPolygonShape2D> col = p_polygon;
	if (col.is_valid()) {
		Ref<ConvexPolygonShape2D> ret;
		ret.instantiate();
		ret->set_points(_get_transformed_vertices(col->get_points(), p_alternative_id));