^ FHWA would want the mileage and exit numbers to follow I-87 and I-90, not the Thruway, which is probably the reason the Thruway Authority is so resistant in the first place. I doubt they'd care so much if they could number the exits 1A-495. Unlike NYSDOT, the Thruway doesn't do reference markers, so everything they have is likely inventoried according to milepoint from the NYC line. If they were to switch, suddenly all their records would be wrong. I would think it would be easy enough to set up a conversion table, especially with everything computerized these days, but institutional inertia is real.
With the recent switch to AET and their insistence on spamming E-ZPass statements with every gantry read, there is no longer any need to keep the entire former ticket system on one numbering system. Further, that "multiple exits in a mile" situation hardly ever happens on the mainline north of Yonkers (where it would honestly make sense since exits 1-5 are basically blended anyways) - and where it does, the exits already share a number with alphabet soup. That said, the Thruway clearly has no interest. Recent sign replacements don't even leave open the possibility without replacing exit tabs or even the whole sign.