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.

The signal will often go green (or in the case of this line, ATC will show that the train is cleared to proceed) prior to the actual departure time. This is because the trains are not allowed to close their doors until they have a departure signal, so this has to happen well before the actual departure time. Depending on the station configuration and signalling technology the signal clearing may simply occur automatically once the line ahead is clear, so it's up to the train driver to ensure that they don't depart too early.

Japanese train drivers are trained to the extreme, with periodic auditing by the trainers that involves being timed with a stopwatch as they cover the speedometer. https://youtu.be/xzkU6tmdImY?t=205

The high punctuality isn't necessarily without its faults; it creates a high-stress environment to adhere to schedule. 106 people died in a train crash that is hypothesized to have happened because the train was 60 seconds late. https://en.wikipedia.org/wiki/Amagasaki_derailment

There’s a limited amount of computer control, you have people checking to see that the platform is clear and it’s safe to leave. Meanwhile, the computer is controlling a physical system and it’s not like the control will be perfect… everything from weather to mechanical failures will affect it.

They have a driver.