This isn’t in the same category as burying a new train line. I lived around just the Hudson Yard water and electric expansions when those happened. It was years of increased noise, traffic and litigation.
Straw man. Nobody claimed these were existential threats.
OP said "I wouldn't be surprised if cost/passenger over useful lifetime still shakes out better for the trains." I'm saying I wouldn't be surprised if the opposite came out–take the costs of the disruption and time value of money into account, and building a new train line anywhere in Manhattan is a worse use of resources than (a) increasing capacity on existing lines, a veritable forest of low-hanging fruit or even (b) eVTOLs.