We're likely to see changes around Walpole junction with the DT work, and it looks likely that Walpole station will be rebuilt as well. (With Natick Center and Winchester Center both under construction, it's the highest-ridership station that's not accessible.*) Given that the MBTA has indicated willingness to do gauntlet tracks (Winchester Center is getting one), it may be possible to have two passenger tracks through the tunnel, plus a gauntlet for high freight.
*2018 count was 744 daily riders. Other >400/day stops that aren't accessible are Franklin (633), West Medford (628), Wellesley Square (626), and Wakefield (483).