OP doesn't provide specifics, but the fare difference he quotes suggests to me that his sister & BF were holding discounted tickets on a Regional and that the next train was an Acela. I suspect that had they rebooked on the next train of the same category, e.g., Regional, the upfare would have been a good deal less.

SDC is not relevant here. This wasa later train, not an earlier one. Moreover, Amtrak fares, at least on the NEC, are largely time-of-day. If you stay within your band, the price difference won't be much. But, if you change service type (Regional to Acela) or non-rush to rush-hour, the fare will certainly rise and by a goodly amount.

I can't see Amtrak altering a pricing structure which seems to work quite well or to permit SDC which would encourage gamers to buy the cheaper fare and SDC to the more expensive train.