He and his entourage typically occupy the First Class Car, but today they might have done Business Class. Who knows? And no, it was not a special train. It was a regular service train AFAICT. I am also almost certain that he was pre-boarded and secured before the plebeians were let in
It arrived 2 mins late into Wilmington.
The live feed on NBC clearly showed him and his traveling party getting into a Business Class car. The announcer was savvy enough to know that BC was not the premium level of service on the Acela, and noted that. Although I suspect most people watching who don't use Acela would probably assume there are three classes, since it's natural to assume that Business Class would be a level above coach.