I'm coming from the Boston _area_ because I can't afford to live in Boston or Cambridge. But guess what? There are comfortably sized houses available already under $400k 20 minutes out.

Exactly. Inner Boston and SF are not dissimilar, but the real difference is when you go outside the city. You can get a good house in Waltham (for instance) for relatively cheap. The same isn't true today in East Bay at least (and I don't know what other direction it would be true in).