Quick update on my side. I followed the advice of John May here:
And deleted my /Library/Preferences/com.apple.windowserver.plist (do that in single usermode). Everything has been working perfectly since then (more than a week now).
I can offer a pragmatic approach to making it work, though it's not really a "fix."
I summary, if I walk into my office and plug in my Thunderbolt monitor without opening my MacBook Air, odds are none of the attached USB devices or Ethernet will work. I last posted a reply saying that unplugging/plugging the Thunderbolt would fix the problem, but longer term it turned out to be inconsistent.
In my hands, all the devices connected to the Thunderbolt monitor now work every time.
It's a pain in the arse, but until Apple fixes the problem for real, it's a practical work-around.