A couple of things are wrong with this:
1. CAHSR does parallel two freeways: US-101 within the Bay Area and US-99 in the Central Valley. The latter was subject to criticism and controversy because the original route billed to voters was a cheaper I-5 alignment, but I-5 bypasses Fresno and Bakersfield which US-99 directly intersects. Since CAHSR actually has to make money CHSRA chose to push through those cities despite the higher real estate costs. It's proven useful as a political tool as well; as CHSRA begins to figure out how to actually kickstart service it is likely the nearby San Joaquins will use their trackage. As the SJQs serve Fresno, Bakersfield and others along US-99 this is the justification for such a route.
2. CHSRA doesn't take rich people's property, Caltrain does. Caltrain has also not done a lot of it yet because they had to fight the lawsuits against their existence, CHSRA's existence, and their electrification project first. It's also likely that Caltrain won't need to as the most viable spot for passing tracks (between Hayward Park and Redwood City) was already grade separated in 2004 for their Baby Bullet trains which make them a lot of money.
3. CHSRA straight up eliminated it's planned viaducts for San Jose and Los Angeles citing the cost. In particular, the big viaduct planned for I-280 and 87 within San Jose. The remaining viaducts are to connect between Gilroy and Merced, where required tunnels are the larger problem.