Is your suggestion "we should do the status quo, except the bridge and tunnel commuters should be confined to tiny high-rise enclaves clustered around train stations strung out over a hundred miles"?
It's the people who like density restrictions who keep trying to force people to build high rises next to train stations. But that's the thing that doesn't work, because high rises cost significantly more per unit to build and if you constrain where things can be built like that then the cost of land in the few areas that allow multi-unit housing gets out of control because of the legislated scarcity.
So the availability of housing 100 miles away still affects the price, because there are still people (e.g. retirees who only go into the city once a month) who would choose a longer distance for a lower rent, or who prefer to live in a lower density area even for a similar cost, and giving them a place to get that means they're not bidding up the price in the city.