Many people seem to believe that keeping your 2FA keys in an un-backupable mobile app and away from your computer is safer than keeping it in your backupable and multi-device password manager.
PyPI doesn't list desktop solutions because I made that list back in 2019 and didn't think to list them. If you have some reputable desktop password managers that support TOTP that you'd like to see listed, you should open a PR for them!
You are certainly far more qualified than I to know which desktop password managers are reputable.
I only installed KeepassXC two weeks ago to try it out because several people here on HN mentioned it, and because it was free software not connected to for-profit companies.
It is the only one I've tried, and I've only used it once, to see what it was like.
I think your historical comment omits something. When I made this complaint back in 2019 you replied at https://news.ycombinator.com/item?id=20058199 saying "I've forwarded this thread along to others working on PyPI as part of the OTF grant, and we'll be figuring out how best to explain using TOTP without being too mobile-centric."
That mobile-centric list hasn't changed, and I still don't have, nor want, a smart phone.