Keeping the rail yards there is a waste. Your ideas are based on the assumption that rail travel will increase in the coming century. Now I am right on board with ya'll there but you need to be looking forward, not backward. First off, we can't anticipate commuting patters. At the moment South Station is in more of a need for expansion than North Station. Also, any large scale rail expansion in Boston will undoubtedly include the North-South Rail Link. This seems impossible given the current climate but one day, perhaps 40 years from now, the demand will be there. The need for the rail yards of the 19th century won't be as pressing in the mid-21st century. Much of the rail traffic which were serviced by those yards was either industrial/freight which is not ever coming back or for commuter trains which could be supplemented by expanding layup yards at far out terminals where land is much cheaper.
Keep in mind that the rail yards, all of them, were built where they were due to the cheapness of the land. Even today no rail company would pass up the opportunity to move their facilities to cheaper land and sell off very valuable land for development. Now, if the demand were here today, then NorthPoint would probably be designed as an air rights project (though we all know how easy those are to pull off!) It would make much more sense for any future rail yards to be built further out where land is cheaper. Hell, they could even be built in Everett in that industrial no-mans land.
