For NJ transit trains, a passenger is required to pay a higher "peak
hour" fee when
it's a "peak hour train" (going to New York/Newark Penn/Newark Broad
St/Hoboken/Secaucus in the morning hours OR going from these five
stops in the afternoon between 4pm and 7pm) AND the passenger is
actually going to/from these stations. It means if I travel from
Princeton to Edison (even on a peak hour train) I don't pay higher
fees, because Edison is earlier on my route than Newark or New York.
The same rule applies to LIRR, except they have their own "peak
stops" (one is New York Penn,
another is Long Island City, I think). So, I keep peak hour flag for
each trip and for each stop in a particular schedule. MBTA says (I
called them specifically to check this) that peak hour trips apply no
matter which stops you're visiting once it's a peak hour train. In
this case, I have to mark every stop as peak hour stop. But they also
told me that MBTA does not charge higher fees on those trains. It's
just to inform you that there are many people expected on those
trains. I have no way to verify this because I'm not in Boston. The
MBTA website, overall very impressive, does not provide much detail on
this.
Yuriy