Not totally off the beaten track, but Modica and Scicli are also down in the SE corner of Sicily.
The historic part of Noto is truly tiny, and the town is very close to Siracusa. It's definitely worth a visit, but there's a lot more to see in Ragusa. The Sicilian trains are not noted for their speed, yet it only takes about half an hour to get to Noto from Siracusa. Rather than going to the trouble of changing hotels for just one night there, I'd plan to drive there in the morning, see the town, and then drive on to Ragusa, possibly stopping in Scicli or Modica (conceivably even both if you get an early start) on the way. Spend two nights in Ragusa and you've still saved a night to use elsewhere.
To pull this off without risking your belongings, you must leave nothing visible in your car while you're off sightseeing on foot. This is not just important in Sicily; the need for this practice applies everywhere. In addition, you must not pull into a parking lot, open your trunk, and place anything in it. That must be done elsewhere.
Are you flying out of Catania? It has an attractive historic district.