If you're putting stations into every major town, roughly 30 miles apart, it makes little sense to build things like curves with a radius of over 3.5 miles (~ 5.6 km) on a viaduct, comparable to open-line track radii in France for TGV lines, just outside of Fresno's station where you're going to slow down to 0 mph anyway.
This kind of silliness is why they're over budget. The most acute impediments to long-distance rail in California is the lack of dedicated, quality track along which a trainset could speed along between towns without regard to freight, so it would stand to reason to solve that part first, while leaving a bunch of expensive niceties for later, when enough appetite for them has been built up.
When France built the TGV, or Germany their equivalent, they didn't rebuild their downtowns to accommodate high-speed tracks; this is a uniquely American fetishism the same way the US took interstate highways into their downtowns in the 60s.