People have a habit of arguing online that this would replace people's commutes.

Which, to be fair, people online have a habit of just arguing past each other.

It might speed up the commutes of people coming into the bay from Gilroy, and it might make Madera a somewhat-viable commuter town (if you don't mind 2 hour commutes), but I can't imagine many people using it for daily travel who aren't already well-served by Amtrak/Caltrain