WOW! Excellent question. I just put in BOS - MIA and was given the choice to take 2153 connecting to 91 (SS) or 2159 connecting to 97 (SM). It is interesting, though, that taking the acela over the NER increased the fare by a pretty decent amount. For two people, it would be $562 to do the acela or $352 for the NE regional. I'm not sure its worth $100/per person to take the acela the 4 hours to NYP instead of the regional when connecting to a LD train.
Edit: I should add that the connecting point was NYP for these as well.
I wonder if this means this will be allowed for AGR purposes? Can you imagine being able to redeem the above trip for 15,000 points in a roomette and getting to take the acela? That would be a GREAT reward redemption for TWO people, considering that a BC seat is 8,000 points each, right?