As to the geography, note that one of the versions calls the train "eastern" rather than "eastbound". However, either reading makes it unlikely that the trial took place in Boston; Charlestown at present is part of Boston, and at the time would have been just to the north of it, so that a train would not have been required.

There was indeed a prison in Charlestown -- the one at which Sacco & Vanzetti were executed. Its site is now occupied by Bunker Hill Community College.