Because interfacing between Blue and NSRL would be a nightmare. NSRL, out of necessity, is going to be well below all of the rapid transit levels. Take a look at this profile drawing:
NSRL ends up 50 feet below Blue at the point that Blue crosses it, and on top of that, on the CA/T alignment that's pretty much right where Aquarium station is. So in order to hook into NSRL, you've got to somehow junction off of Blue between State and Aquarium, bang a left and also descend to somewhere between 30 and 50 feet lower somewhere between Aquarium and South Station. There's no room. It's also a terrible idea to branch Blue before State (Orange) and GC(Green), assuming you're planning to through-run up to Wonderland/Lynn.
What you could do, if we're committed to the bit, is tunnel under South Station from the Fairmount, run up Congress in a new tunnel, portal up to elevated after Haymarket, and find your own way over to Chelsea from there. That, too, is firmly in Crazy Transit Pitches. But mixing NSRL, Fairmount, and Blue... too many blockers, not enough benefit. EMU-ing Fairmount would be cheaper and faster.