What about it? I've never heard it described as a better internal transit system than the Bay Area has, just a better system as part of the multi-authority feeder into the transit system for the New York City metroplex.
If there was an adjacent New York City-scale metroplex into which the Bay Area fed, it would have very different transportation demands and needs -- and likely a very different transit system -- than it does.
Is BART an "internal" transit system and not a feeder system to/from SF?
NJ Transit is not solely a feeder system into NYC (that's what PATH is for), though that's probably most of it: https://www.njtransit.com/pdf/rail/Rail_System_Map.pdf . Is Oakland not analogous to Newark in this system?
If there was an adjacent New York City-scale metroplex into which the Bay Area fed, it would have very different transportation demands and needs -- and likely a very different transit system -- than it does.