Another issue with the SoCal separations (also with Caltrain and the like) is that the area is quite fully developed. That means the separation isn't a simple over or underpass; it also has to handle intersections with parallel streets, big retaining walls to minimize right of way acquisition, if going over the tracks being higher than normal to clear HSR in some places, multiple (more than 2) tracks for main lines and rail+transit, space for peds and bikes that isn't there now (at least not officially), and generally all sorts of gotchas that occur when there are already people and businesses around. Then there are the issues mentioned about keeping streets open during construction, which complicates which is more expensive and takes longer which is more expensive. And "since we're building it anyway" making it bigger and wider and fancier looking than it really has to be right now.

A greenfield separation in a rural or lightly developed suburban area, that's just a bridge over 1 or 2 tracks, or even a tunnel under, is still relatively inexpensive ($10mil would be gilding it a bit for 2 lanes; about right for 4). Too bad LA and the Bay Area don't fit that description any more.