[jaredsohn]

They likely don't allow buying tickets on the train because otherwise people could ride for free if nobody checks.

Having a Clipper card in the situation you described is great since you can scan your card quickly and at least make the train. (You still might get screwed over if you forget to scan out, but assuming your time has a decent monetary value, it is a risk worth taking.) Personally, this is the only situation in which I use Clipper for CalTrain. If I used CalTrain all of the time, I'd get the Clipper monthly pass. For one-offs where I have to wait awhile anyway, I'll stand in line at the ticket machine.)