Computer control is nice but it's one tiny piece. If wayside infrastructure fails during rush hour, trains are going to be delayed, so they have to assure that won't happen. Station dwell times are another big issue that computers don't have any control over (the train can't leave when someone's backpack is caught in the door).

Computer control is more of a safety issue than a reliability enhancer. Computers are pretty good at stopping trains before they crash into another train or rocket off of a curve some idiot took at 80mph, but not so good at driving the train at its safe limits. Ever ride BART? It's been fully automatic since its inception (in normal operation, drivers have an e-stop button and make announcements) and it isn't setting records for on-time performance.

I think the fascination with Japan's on-time record is a little overblown. I went to high school in Tokyo and I was late plenty of times due to train problems. Snow? Schedule is fucked for the entire day; trains canceled, trains late. Someone falls in front of a train? You're not going anywhere for an hour. As a rider of the New York subway system during the "meltdown", I can tell you that you can absolutely do worse than Japan. But the MTA was still happy to hand out vouchers explaining why I was late to work.