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.