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I am a current PhD student in Pittsburgh and grew up just north of Bellingham. I like it here a lot, and think it fits most of your criteria. It should not necessarily be your #1 pick, but I think it's a mistake that it's not on the list at all.
AMA, but, for starters:
- affordability. Pittsburgh is cheap. It is cheaper than Detroit, but somehow nicer. I own a house as a PhD student and that is not terribly unusual. (I do not know anything about the property market for an entire campus, though.)
- pleasant environment as a research scientist. I bike to my office through a beautiful 400 acre park. The city is eminently walkable and I don't own a car. It's not as pretty as the Puget Sound (which is exceptional), but the city is in a forest-hill-river ecosystem and there are more than enough places to go on contemplative bike rides, trail walks, etc. There are a bunch of other technically minded people in the city who are interesting to talk to, although it is of course smaller than Boston or the Bay Area.
- positive culture/governance. My sense is that the political climate here tends pragmatist and positive-sum. Overall it feels sane here, and while the city has some genuine problems, it feels like the trend line for the future is optimistic, and I don't worry that the city's leadership will get sucked into deranged nonsense in the near- or long-term. Suffice to say this is sort of notable for this country.
- lower X risk. there are no natural disasters worse than the occasional snowstorm. It is supposedly the least disaster-prone major city in the US, and was almost chosen as a location for Alcor on this basis. The long-term prognosis for climate change is that the area will eventually have the weather of, say, Nashville or Atlanta today.