The second reason is closer, but not exact. Caltrain has a variety of different types of trains, some stop at all the stops, some stop at only a few. Here's the scenario: there is a fast train then a slow train. Your normal schedule doesn't allow you to get to the station on time to take the fast train, so you normally take the slow train. If both trains are behind schedule, you might be able to make it to the fast train, and since it goes faster you might get to your destination earlier than normal.
