* There won't be $20-40 tickets on the SF/LA route, because (a) capex costs will be much higher than the white paper anticipates (it costs its el line at 1/10th the going rate for viaducts and its tunnel at a tiny fraction of any other tunnel, even given the narrower tube --- not to mention an extremely optimistic projection for much much tunneling will be required, projections lower than those for the Tejon Pass HSR concept, which runs at 1/3rd the speed or less and can thus follow a tighter course) and (b) ticket prices have to account for opex as well, which will be substantial; having built the thing, it does not simply run itself.
* Land in the central valley might be cheap, but the ROWs you'll need to do anything from Chicago to NYC won't be anything resembling cheap. Note that the "hyperloop" painfully acknowledges this, by terminating in Sylmar, on the far northern outskirts of LA, because integrating more thoughtfully with LA's transit system would have been prohibitively expensive; similarly, the "SF" end of the route is actually San Leandro, which is an hour easy from SF in traffic.
Something else to consider though - those prices are for ridership levels that you could expect by connecting SF and LA. If you start to link up more points (Vegas, San Diego) the utilization of ALL the lines increases, which means you're amortizing the capex over more passengers... which helps a lot given the small fraction Opex will constitute.
To your second point, are you sure it'll be prohibitively expensive to integrate it into the city transit systems? As an elevated system I don't think it'll necessarily cost that much. I suspect it was omitted as much because it'd be expensive in concept evaluation time to sort the details of the integration as because they're just crazy expensive. Is it really that hard to get 2 x 3m tubes on stilts with a foundation every 30m out of a city? It's a very different proposition to putting in a new ground level rail line.
HSR goes from city center to city center because that's where people actually want to go. Not only that, but it's much cheaper for them to get to city centers, because they can use existing rail lines, which is something blue-sky proposals like Hyperloop can't do.
The point is that the transit time from SF to Hayward is part of the SF/LA transit time. That's all.
edit: Oh, I think you're sort of a mentor figure to one of my friends from kindergarten (and a board member of my startup nonprofit...) HN isn't really the best venue for a nuanced discussion, if you'd like to talk about the problems with CHSR and why comparing Hyperloop to CHSR official figures is charitable to CHSR - feel free to contact me personally!
It gets even more attractive once you link up the dots between areas. If you built a hyperloop between NYC and Chicago, for example, you'd probably route it through Detroit... which means you also capture the NYC-Detroit and Chicago-Detroit traffic.
For instance, the Chicago-New York route is roughly 800 miles, which is about an hour of hyperloop time. If the tickets were still priced in the $20 range each way, just think of how many more people would travel between the two cities.
People could live in Chicago while commuting to work in NYC. Others could live in NYC and impulsively decide to travel to Chicago for a fun night out on the town. Surely, the route would increase in popularity - perhaps vastly so.
What I love about the hyperloop is that it's like a physical embodiment of the internet - shrinking the geographical distance that separates us.