Wow, you actually might be better at my game than I am! Beating a boss that strong without potions is actually really impressive, fantastic work.
A lot of the buildings will be reopened in 0.3.7- I didn't have the time to get to them all, but that's part of the plan. (Presumably everyone needs some time to move everything back in.)
Spoilers Ahoy:
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Some earlier dialogue (again, probably a while back) established the original Cloudborn were created as a result of Forruno experiments with Wind magic, presumably before Orb-related shenanigans started. Sonon was one of them. They were citizens (until backstory happened).