Well, I have some good news and some less good news.
I made a script which successfully deletes all of the (non-smart) playlists in iTunes, and it works brilliantly. I need to clean it up a bit before I post it publicly at all, but that is done. The other good news is that running this before a MCiS sync does absolutely fix the sync problem in MCiS.
So, now for the less good news...
Using this completely breaks my usage of MCiS. The issue is that when you delete all of these playlists, and then run the MCiS sync, they get recreated as new lists. The issue with that is that if you use any of these lists to sync to an iOS device (which is why I'm using MCiS), the saved sync profile in iTunes for your devices "loses" all of the lists (they all become unchecked throughout the Device Sync UI in iTunes).
For me, this is an absolute dealbreaker. I have a whole set of lists used for various purposes, for 6 different iOS devices, and so I'd have to go back through the iTunes UI and re-enable the lists in all of the various areas where they're used for device sync (Music, Audiobooks, Video, etc).
So... That's no good. I'll still post my script since it is almost all done. But... Boy that's a bummer. I guess I'm going to fire up Visual Studio and see if I can get the issue fixed in prod's code!
What will REALLY tick me off is if I do this, and then Apple releases iTunes 12.7 or whatever that either: (A) completely removes the COM API and breaks this once and for all, or (B) they fix the issue themselves and the whole thing was pointless.
Sigh. Can't prevent that, though, really. Hopefully it is something dumb and easily fixed.