I think the so-called Richmond Specials (there are at least 2 on my block--I didn't know the name until reading that article but recognize them everywhere) have aged enough that they've become part of the accepted architectural landscape.

Anything new will be hated by people. But why spend a fortune to be hated when you could spend much less and be hated all the same. San Francisco requires almost every building to prominently incorporate bay windows as part of the facade. (Richmond Specials lack this, which is why they stand out.) Every era of housing does this differently. As long as the pre-fab does it at least as well (very low bar), they'd fit right in. Plus, stucco is an extremely common street-facing exterior finish, and all the pre-fab stuff seems to have similarly textured exteriors.

I'm no architect, but I think if you can mimic the Edwardian or Spanish Revival styles (which are already quite simplified and boxy) which dominate much of the city you can grease the wheels. I don't understand why architects expend so much effort trying to do anything else; all it does is invite more attention.