Answer: you just have a bigger time zone table, like
https://www.netburner.com/wp-content/uploads/2020/02/Compara..., where you can see that A (which perhaps stands for Albany, N.Y.) is 14 minutes ahead of Washington D.C., and B (which is perhaps Baltimore, Md.) is 2 minutes ahead, so this rather fast train will arrive at 2:48pm (12:00 noon + 3 hours − 14 minutes + 2 minutes).
It’s really no different from the coarse-grained time zone system, just more complicated because you have much bigger tables.
(I’m pretty sure I’ve seen a picture of a railway’s time zone table from before the 1883 change to coarser time zones, sorted by station, with most deltas being one or two minutes, but I can’t find it now.)
