For instance, I'm in PA (sigh, although I love where I live), and there are 3 in-person methods: Optical Scan, DRE (Direct Recording Electronic), and Paper Ballots. I voted by Paper Ballot in my rather small little township.
How is this determined state by state? Would it not make sense if in-person voting used the same method everywhere?
You are correct. Only the state legislatures can set the election laws for the state. Counties cannot legally come up with their own ideas. Not saying they don't break the law and do it. But the law is the law and counties don't write laws. The US Constitution does not give counties the authority to do so.
One caveat. If the state legislatures write a law that gives counties the authority to come up with their own system, then the counties could do so because it is legally authorized by the state legislature. Another example of how each state can do their own thing.