All Amtrak trains (except trains to Maine) go to South Station. The Maine trains depart only from North Station. And there is over 1 mile between the two stations!
Yep, and if a novice traveler asks for advice and is told to "get off in BBY and take MBTA to BON," it's just going to frustrate him, and probably make him go looking for someplace that's more helpful. "Get off in Back Bay and take the Orange Line to North Station," isn't hard to type at all, and would be the courteous advice for someone who's not a thoroughly hardcore Amtrak traveler.
But like I said, I don't really expect habits here to change. It's unfortunate, though ...