As the article points out, the difference in cost between these two routes is pretty small in the grand scheme of things; more than two-thirds of the costs associated with the project are at either end getting in and out of Los Angeles/the SF Bay Area. On the other hand, as the author points out, building the route through the Central Valley population centers has a number of advantages (political support, having a useful rail line before the entire project is complete, etc. etc.)
If you use google maps to find the distance between Los Banos and Tehachapi. Via I5 is 210 miles. Via HWY99 is 223 miles. So a 13 mile difference. That's 5-7 minutes at high speed rail speeds.
And you are right the extra cost is minimal. It's probably $10-15 billion.
My thought about the grade separation costs and my beef is. One is those grade separation projects need to be done anyways. The beef is why is the high speed rail project paying for road infrastructure. That should come out of gas taxes or something.
