It was my understanding as well that the Type 9s can't run in the mixed-traffic portion of the E because they don't have the pop-out stop signs on the doors (a design flaw the T didn't see coming until the trains actually went into service).
But even if Type 9s don't run the E, they can still serve a portion of the GLX on the D to Union.
Yeah there really isn't much dead space under here. The bus loop, bus shelters, bike racks, and station entrance itself will all be under the overpass, as well as multiple street grid connections. I expect the street level space underneath the new Lechmere to actually be pretty lively.