The MTA only bought the right-of-way as far north as Revere St., and that's what the MBTA owns. Beyond Revere St., the utility company bought the easement in Revere from the trustees of the BRB&L
I share everyone's dismay at:
1) Our lack of regional planning
2) The break in the ROW at Revere St
3) How short sighted not to acquire the BRB&L ROW all the way to the tip of POP, across the channel and on into Lynn
4) The encroachment on the ROW...all cramped and looking bad even for a bike path
But the MTA / MBTA seem to have nonetheless stumbled into an OK set of options that involve crossing back to the Commuter Rail ROW and paralleling it into Lynn, rather than entering Lynn in the backyards of Route 1. (or splitting the line back south of Wonderland).
The MTA could not have forseen the trouble of crossing wetlands, but there is clearly still the open space that permits crossing the marshes either immediately north of Revere St, or anyplace in the long stretch north of the Rent-a-Tool and south of Mills Ave.
Even if the MTA had acquired a "full width" ROW, I don't really see how you'd get away without enormous offsets to the community.
Given how closely the longtime abutters abut the ROW, and how slender the land is at it northern tip (where the US 1 drawbridge crosses into Lynn from Revere), I think the NIMBYs would have an unusually strong case that they already support more infrastructure per acre, and that a two-track surface subway would overwhelm it.
While I'm usually a guy who says "what did you think those tracks behind your house were for?", at this point the tracks have been gone since 1940 and we're getting to the point where the railroad has been abandoned for longer than it ever operated. Many of the houses seem to date from 1910 or later, so for nearly 80% of their 100 years, there's been no railroad.
On the BRB&L north of Mills Ave, you'd spend a lot of engineering $ on a bridge and a whole lot of hearings proving that it can't be put in a tunnel. I'd guess you'd practically have to build a concrete box around even a surface line to mitigate the noise--on "heavy rail" trains, its got to be worse than even the tall sound walls they've proposed for the GLX through brickbottom.
In the end, I think Lynn is going to have to have a station that looks a lot like the Orange/CR in Malden Center, and that comes right up through GE/Lynn Works.