Welp, those thank you notes did rattle some cages alright, but not quite exactly the way I wanted them to. Apparently the "runner-up" company (Company 3 in this current saga) will not be making an offer because they were interviewing someone else in parallel and they offered them first and they accepted.
It kind of burns, but I'd rather lose out in this type of situation (the VP I've been working with was falling all over himself telling me how close of a decision it was) than just for spurious reasons or failing some stupid coding test. Of course he couldn't tell me the specifics, but this is what happens when you have 1 available position and multiple applicants.
(my guess is that my age and experience and perhaps some of the questions I asked about the culture gave them just enough pause to make the offer to a younger, lesser-experienced-but-more-easily-told-what-to-do person.)
And, this is the company where I had some ethical as well as cultural concerns as potential down-the-road problems, so now that little bit of cognitive dissonance has been cleared up for me.
Anyway, it stings a little but in the long run, it's what I really wanted to happen. Now I can just focus on doing what it takes to get the job that I really want at Company 1.