It will be interesting to see how the plans work out. Currently "Track 61" connects to the T's Old Colony line just south of Amtrak's and MBTA's commuter rail maintenance facilities, where a train would have to change direction to reach South Station or Back Bay. Back Bay would require an east-to-west crossover move across five or six tracks to reach the wye to head west. The T's Red Line rapid transit and its shop, not to mention a couple of developed blocks, are in the way of a direct connection.
Today's (6 Sept. 2013) Boston Globe has an article about using a rail line from Back Bay Station, through South Boston rail yards and a lightly used freight line to connect the Seaport District to the Back Bay. More info at http://www.bostonglobe.com/business/2013/09/05/state-begin-innovative-rail-service-between-seaport-district-and-back-bay/oHUinYj30lzOV6KNCQUMEJ/story.html?p1=Well_BG_Links
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