^ Most of the buildings you are citing have ready access (or the potential) from the cross streets. Very little actually fronts on Herald or Marginal. It is much easier to reconfigure than you are claiming. It just doesn't give you your pet subway. This area was all ratfucked, as you term, by urban renewal -- and nothing faces the Pike.
Ink Block, for example has ZERO access from Herald.
You haven't answered the question: why are we reinventing the wheel? For me-too pet projects' sake??? What is the value proposition of this? Have we answered the question WHY the air rights haven't been sold with a definitive answer that "the grid sucks...and A, B, C, X, Y & Z potential developers have rejected it because of the grid." Point to concrete examples stating that a reboot Must Be So or they will never attract developers. Have these parcels even been seriously floated? Or has the clownshow of decades wasted trying to get something/anything approved on the blocks west of the Pru decking punted the easterly parcels to the back of the priority line? How is that a physical constraint instead of institutional?
Second...there's an orderly street grid that's been in place for 50 years for specific purpose of fronting air rights on those blocks. There's load-bearing retaining walls for holding up the air rights. It's all been completely paid down by 50 years of Pike tolls. The only cost are the deck girders themselves, presumably to be paid for with some sort of public-private financing plan that amortizes cost over multiple decades, like the Mass Ave./Boylston cover-over.
There are NOT load-bearing walls for holding up a middle street + transit reservation and new building foundation anchors on the middle street.
This pair of jersey barriers between EB and WB carriageways and EB + the NEC are all you have to anchor it to. Look how the Pru tunnel is anchored; thick side walls, thin center that occasionally opens up to
porous pegs at the street overpasses pre-dating the cover-over. The foundations are anchored to the thick/deep side walls where gridded girders on the deck spread the weight distribution all around the block and don't require anything thicker than pegs in the center.
You don't have horizontal or vertical room for
Y-shaped thick pegs to straddle a boulevard centered over 100 ft. of Pike with enough strength to hold the outer boulevard lanes, much less outer lanes spread out further by a center transit reservation. You most certainly do not have ANY sort of load-bearing capability to anchor building foundations to that center road where the street-facing foundation are literally suspended midair over the center lanes of Pike EB and Pike WB. The deck girders won't support themselves. Structural engineering does not work that way. If you nuke the surface...you are going to have to nuke the Pike underneath, nuke the side walls to move WB under Marginal and NEC + EB under Herald so the new center wall can be twice as thick, twice as deep, and be capable of anchor the building decking's weight distribution exactly the same way as the old street grid. Total reinvention of the Pike Extension wheel. And lo and behold...massive tunneling under Marginal! For somebody's more expensive idea of a pet project. And cannibalization of the transit build studied for 40 years in favor of ops-inferior surface running. Throw every argument out the window that this is non-invasive to the cut below. It's a total do-over of the cut.
Finally...nuking the grid WILL ratfuck abutters like the Quincy School. Don't play the "it's not too many abutters" card, because that shucks the question of how important the abutters are. In redev-beleagured Chinatown residents' view the Quincy School is the red line that shall not be crossed when mere redev crosses over into Urban Renewal: Payback Time. The school caters to Chinese students in the neighborhood--the only one equipped for such bilingual and bi-cultural needs--and has long been one of BPS's best performing schools. Take that away, force a rebuild or move, or force students to walk down a claustrophobic alley replacing Marginal to get up and down campus from the main building and bus/Orange stops @ Washington to the Upper School on Tremont...and that is tantamount to re-declaring war on Chinatown. You won't get a single City Councillor in support of that...and for whatever you think of the shiftless Council, it is their purview to stick up for a neighborhood that feels it's getting pushed around.
Also...if you don't pull a "Hold the phone!!! We're doin' a reboot!" ASAP to everly developer licking their chops at the squat-garages blocks of Herald, that property's going to get flipped in a period of few years to complement the Ink Block with street-facing dev. It's a moving target, not a static 2D canvas. This concept is going to ratfuck a whole lot more abutters--ones with big money recently spent behind them--before you even have a chance to float this do-over to the public like a lead balloon.
This is not the real world. It's not. And it has no chance of graduating into the real world if the value proposition can't be articulated better than "fussin' 'round with the grid for neat-freak's sake." The argument has to cite damning, fatal flaws in the 1965 canvas that render air rights dev utterly impossible and OVERPOWER opposition. +1 points for general elegance isn't enough. Not within light years of enough.