Comment by lmm

> if the stations are split into two boarding areas like I've proposed then the front of the train behind was already scheduled to come to a stop before reaching the rear of the train ahead of it.

You can have one train reach the station sooner because it stops at the back of the station which is behind the front of the station, sure, and that's safe because the train is still 3 minutes behind the train in front. But that only works once. The next train has to be 3 minutes behind the train that stopped at the back of the station (and 6 minutes behind the first train), so unless you've got an infinitely long station you're not improving your overall throughput. And you have to give back the time you saved as soon as you want a train to stop at the front of the station again. Skip-stopping doesn't help, in fact if anything it makes it worse.