There definitely is some smokiness after a train passes, but not as bad as either platform area at Back Bay. The 'tunnel' section is much shorter and with a more direct path for wind to clear out fumes, and locomotives are usually under Beacon Street (ie near one end). There's also somewhat fewer trains than the NEC platforms at Back Bay. Additionally, much of the problem with Back Bay is that the ventilation fans and louvers have been frequently broken/unused.
That said, I do hope that they have ventilation planned, and I look forward to the day when everything passing through except maybe the Lake Shore Limited is electric.