Welcome to aB. I know you are excited and want to revive old threads to talk about some of the things you are excited about, and that's great! Unfortunately, with no news to report and questions/suggestions that have already been answered, it is frustrating to see a bunch of these revived for no reason. Anywho, welcome aboard.
As to your suggestion, we could do a lot of things, technically. Unfortunately, underground super-highways only make any sense on a cost-benefit basis when there is a LOT of benefit. Here, there is little benefit to expensively burying an overbuilt urban feeder route. On top of that, Back Bay is completely fill, so the engineering difficulty/cost would be through the roof, and potentially unfeasible. So maybe we couldn't do this and maybe we could, but either way, we probably wouldn't to.