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There were previously stations with enough clear passenger demand to justify express service to those stations, but which weren't on the express line because historically they had fewer passengers. Caltrain didn't want to slow down the express line by adding stops, but now that they have the opportunity to add the stops while also making the service faster they did so.

The track still has a hard speed limit of 79mph from the rails themselves, so much of the savings is in acceleration and braking.

Since adding stations costs less time now, I guess they decided these extra two were worth it.

edit: rules around level crossings may also have something to do with the speed limit.

The increase in riders might be worthwhile and part of why Caltrain can now have off-peak trains “run every 30 minutes, rather than every hour”.