Well, I'm traveling on Acela business class, so I don't have the accommodation upgrade issue to deal with.
I went ahead and purchased the ticket from RTE rather than PVD...I'm traveling on Wednesday so I will update everyone with my success/failure. I figure the worst that happens is that if the ticket gets cancelled as a no-show I immediately buy a new one on my iPhone, but I am with the majority and doubt that will be the case.