Not to mention Amtrak Lake Shore Limiteds and Inland Regionals - my understanding is that even a Dual Mode Airo running on the Inland is likely to pull into South Station in Diesel mode, as the Worcester Line tracks aren't wired up at Back Bay, only the final ½ mile in the S. Station terminal district. (Assuming the Airo has to swap at a stop? I haven't seen anything to indicate it can do it in motion.)Enclosed spaces are a pain-in-the-ass for RR operations. Even in a fully electrified future you want considerations for a diesel rescue loco or diesel service substitution for overhead wire maintenance to be able to access the station. We don't want a situation where complex and draconian operating rules are required like in Grand Central or Penn Station to get even *one* rescue or work-shift diesel into the platform space. That'll be required for NSRL by necessity, but there's no reason to breach that subject beforehand. Surface South Station will always have to be open to the elements.
Besides, diesel stuff is going to continue using South Station even if regular electric service comes to all Commuter Rail lines. Cape Flyer will malinger as diesel until we muster up enough daily commuter service to Hyannis to justify electric. A future Newport Flyer will probably always be diesel...and so on.