No, I think the more simplistic MTA Metro North/Long Island Railroad model should be used.
That is, each train is marked "Peak" or "Off Peak" and the (zonal) fare for each are considerably different. But the fares are on the printed schedules and you can work out in advance how much a journey is going to cost, very easily.
On Commuter trains each train is either choc-o-bloc with people fainting, or running at a fraction of capacity (or empty), so a Peak / Off Peak distinction Metro North RR style should make sense.
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