My understanding is rail tariffs to transport subway cars are far higher than trucking, especially given the relatively short distance in this particular case. MBTA has not received rapid transit cars by rail since the late 70s/early 80s (Boeing LRVs and Hawker-Siddeley Orange and Blue Line cars). There are no current direct physical connections between the national rail network and MBTA rapid transit, although their proximity in several locations would make it relatively easy.
The Orange Line has an intact connection north of Wellington.
It's not clear if the connection to the Green Line at Riverside is still intact, but it would be trivial to restore it if it isn't.
The Red Line has a new connection at Cabot Yard built as part of the test track. Historically, a temporary switch connecting to the Old Colony line would've been cut in near Columbia (today's JFK/UMass).