Since the Basilica is free to visit independently, a Museums-only tour makes sense if you'd rather see it at your own pace afterward, or if you're short on time and a combined tour would mean rushing both.

The Sistine Chapel is included either way — it's part of the Museums route, not the Basilica — so skipping the Basilica portion doesn't mean skipping the tour's main draw, just the walk to St. Peter's Square afterward.