The costs are based on Hayward to Sylmar. You can draw whichever lines on a map you want, but rights of way into SF proper and downtown LA are intractably expensive. Again, this is an advantage HSR has over "Hyperloops": HSR can reuse preexisting last-mile right of ways, and Hyperloops simply can't.

One critique of Musk's plan pointed out that the Shinkansen trains were essentially a frivolous novelty until they were brought into city centers. The same thing was true of Southwest Airlines trying to service NYC from Idlewild. You have to terminate transit lines at places people want to go.

Also, the bar you're trying to set for critiquing the Hyperloop is too high. An argument against Musk's plan need not show that it's impossible to build. Rather, the bar is simply that an unproven new technology must have significantly better cost and performance characteristics than HSR. Nobody is going to drop many tens of billions of dollars to build this thing "just because".