I spoke with Apple Tech Support yesterday. She tried a buncha things on her end, some more button pushing on my end, end result is that the problem is not fixed/workaround, it's just different now. Still missing a gob of songs from iPhone -> iTunes -> Purchased. She suspected they were "hidden". She did something at her end to unhide a bunch of them, but not all. I had tried "Unhide All" a few days ago, but it didn't seem to do anything. Today that's gone.
I have provided a buncha data to them for analysis. She recommended that I not put a lotta effort into fixing/workaround at this time. Wait for a bug fix. Then start cleaning things up.
Anything I do now might be a total waste of time because the bug behavior is sporadic and it might break something I thought I had fixed/workaround yesterday.
This looks like a database corruption problem. iTunes has always had issues with creeping crud in the database, but this is a whole new level. It's possible that the hotfix may be unable to repair the database damage, and we'll have to rebuild our music library from scratch.
My experience and recommendation is to stop trying to fix something that's fundamentally broken, we can't find a workaround that doesn't get undone or some other problem manifests when Music goes insane again tomorrow. Imma just suffer through it, use what limited functionality it still has, and wait for a fix. I've wasted cumulatively two whole days on this, and I'm no better off than I was before. Different, but not fixed.