I also think it has to do with the large Commuting block between PHL and NYP. I noticed Rush-Hour Regionals that depart close to the same time as Keystones in AM from PHL ( trains 170, 180, vs. 640) or PM from NYP (137, 55 vs. 655) are priced significantly higher than Keystones.... Even if booking during the 14-day advanced pricing window, I've noticed where both trains 137 and 55 will be over 100$ for NYP-PHL while 655 will be just 39$ (14-day), all three trains leave NYP within 20 min window. When Amtrak runs NYP-PHL 25-27$ "3-day Sales" specials it mostly only consist of the Keystone trips. Regionals (except for evening/night trips) have been excluded from the specials. I think Amtrak does this to get the majority of NYP-PHL people to use the Keystones, saving room/capacity for people going South of PHL.
I remember people saying a big problem with PHL-NYP rush-hour Regionals was that commuters within those two city pairs were filling up the train, leaving no capacity for WIL, BAL, WAS from NYP. But the same trains would then have a ton of capacity leaving PHL,