I would think the best way for Amtrak to handle the high turnover mid-route would be only assigning like 2/3 of the seats, with the 2/3 based on the % of ridership that is going WAS-NYP or NYP-BOS. This would create an open seating section that anyone can claim and a the person buying a PHL-STM ticket won't see sold out when booking online since all the seats are grabbed by NYP-BOS and NYP-WAS passengers. They'll simply be told to grab an unassigned seat if the train is already more than 2/3 full.