I agree that light rail on the surface is probably the most likely path for Boston rail expansions in the future. The cost of going underground is just too steep, and elevateds won't be tolerated.
I was reading an article about Zurich recently and it occurred to me that, in a way, the construction of the Tremont Street/Boylston Street subways may have led to the decline of streetcars and the rise of automobiles in Boston. By getting the streetcars off the surface, it was an early benefit to automobile drivers, who were not a force in 1900 but were by 1930. Of course that may have happened anyway, but, Zurich famously rejected multiple subway proposals in favor of surface transit improvements. And now look at them.