The B&A is no longer a clearance route east of Framingham. I believe they are building/built high-level platforms at Natick, and thinking about the three Newton stations. So will freights have to creep by the platforms? AFAIK the Turnpike Extension bridges are not cleared for double-stack (is this correct?).
Moreover, CSXT commits to continuing to route traffic from the existing CSXT network onto the existing PAR/Springfield Terminal network through Barbers Station and Ayer, rather than using the Grand Junction Branch. If CSXT sees the need in the future to consistently operate using the Grand Junction Branch from Worcester and Framingham, which CSXT does not currently foresee, CSXT is committed to working cooperatively with MBTA to implement capital improvements to accommodate any changes in CSXT freight service.Not to say that it's set in stone, but it doesn't seem likely to me. Increasing clearances at Memorial Drive seems like it might be very difficult. You can't really lower the roadbed because it's immediately adjacent to the Charles River bridge, and raising Memorial Drive (which is already a bit of a rollercoaster through there) might require a major reconstruction of the BU Bridge rotary flyover and associated ramps.