One of the reasons they didn't attempt a 6-car lengthening of Bowdoin is that the structural mods would've ended up dragging it even closer to GC where the emergency exit conversion beckons. As it stands a substantial portion of Bowdoin's platform would remain structurally intact when they do the partial demo for the loop-end straightening, leaving it and a recycled rump of the exit staircase as a level-boarding emergency exit for 3-4 cars. Yes, you'd absolutely be able to build a new station there by recycling the easterly platform remainder and extending it anew to one side or the other. But that'll either put you true-uselessly close to GC...on the order of 300-400 ft....if it stretches east, or pretty redundantly close to Charles if the new platform extension trudges further west. Charles itself has the option for an easterly Blue-only headhouse on the Grove-Anderson Sts. block if funding allows, and that kicks another leg out from under Bowdoin. Because then if you opt to rebuild it post-straightening the works are going to shift further west, entrance-to-entrance on that side is 1000-1200 ft.Yes. GC Emergency Exit is located here.(https://goo.gl/maps/UJmRi6bUZasZRX7B6). Entrances on the "Bowdoinside" of both MGH and GC are a better solution than keeping a curve-crippled Bowdoin. And if we're crazy-wrong, in 40 years, you can come back and do an infill on its site. When they straighten things out and eliminate Bowdoin they should put it in a place that doesn't rule out a Future Straight Bowdoin.
Depending on what AFC 2.0 looks like, you could probably push the front doors /canopy to the headhouse another 50 feet closer to Bowdoin/Sudbury/Bullfinch Place for a psychological win.
And, yes, build/provision MGH Blue as a two-ended platform
I wouldn't hand-wring about Bowdoin. You can do the partial demo and attempt some sort of rebuild later if demand does hedge towards closer stop spacing. But you won't ever get a chance to buy longer, higher-capacity cars without straightening through the loop. You won't get a minimum operable headway that can match Orange or Red's capabilities unless you whack the speed restriction near the loop structure. And outward expansion north to Lynn & beyond or west to Kenmore & beyond is going to be harder to administer unless you even up the asynchronous IB vs. OB speeds through the loop structure. Those considerations are all saddled with complications forever if you don't demo Bowdoin. You're never--for life--prevented from building a new Bowdoin if need be after some healthy debate about whether it's truly necessary points to the affirmative.
Ergo, smash that loop to bits and don't worry about the rest until you've got funding, because all 100-year considerations are covered any which way.