The other thing to think about is what is the alternative - road or airport construction in california is not cheap. Replacing 2 bridges on I-5 in stockton is going to cost nearly $1b alone.
And I think a lot of the benefit won't just come from the main SF LA route, it'll be intermediate stations to SF or LA too. It'll only take 19 minutes to go from Palmdale to LA for example - compared with 1hr+ now. In a way it would have been better to have the IOS be one of those routes, but they are also the most difficult geography.