There actually is not that great a market for air rights over tracks and roads (most of the pike and the NEC have languished for decades, or, when decked, have been decked with public $). Only super-prime sites (eg across from the Hynes) end up attracting qualified projects.
The problem is that decking is so darn expensive and that being without a basement means mechanical stuff takes otherwise usable space above-deck. In the end, air rights are worth a whole lot less than "real" sites nearby.
Tufts, with an HVAC plant across the street, would be the high bidder in any auction, and still I can't see them needing to bid more than $1 because nobody else can affordably develop the site. It looks like a win for the T (better cheaper station), Tufts, neighbors (clustering / mitigating development) and Medford (tufts not reducuing the tax base as it grows)
"Trying to solve congestion by making roadways wider is like trying to solve obesity by buying bigger pants."--Charles Marohn