People do commute on the Tokaido shinkansen, but that is not the majority of its ridership. The numbers I've seen give about 10% of Tokaido shinkansen ridership as being due to commuter passes (and anybody who doesn't use a pass for that would be completely insane), measured by "trips"; if measuring by "passenger-km", of course, the proportion due to commuters is much much lower, about 2%, because commuters tend to travel much shorter distances.

The bulk of the riders are business people going back and forth for meetings etc, and ordinary people going on holidays and the like. The most insane peak periods are around national holidays, especially long ones like golden-week where the trains are often running at significantly over 100% capacity (I've stood the entire way between Tokyo and Osaka, crammed up against others in the car vestibule...).

You're right that the shinkansen prices are significantly higher, but if anything that demonstrates how great the demand would be for a really cheap service (as Musk seems to be claiming, however dubious that claim may be), and thus how limiting the low projected capacity would be...

I still don't think SF/LA are as interconnected economically as Tokyo/Osaka/Nagoya are. You have a lot of manufacturing in that area of Japan, while the big population areas of California are much more separated and specialized. One could live their entire life and career in the Bay Area without any reason to ever visit LA, and the other way around.