

So the two-factor authentication apps shouldn’t be on desktop argument never made sense to me, mobile is the same way.
I think that argument was rooted in the assumption that the phone was a separate and smaller attack surface. The assumption is reasonable if you use your credentials mostly on desktop and only have a few apps on your phone, which was indeed the case for a lot of people in the past.
But nowadays, a lot of people use the same credentials on the phone just as well, and with everything asking to install their app, I’m not sure the attack surface really is smaller anymore. So, if you’re in this scenario, I agree with you that you may not be sacrificing much by having 2FA on desktop.
And, of course, 2FA, even in the same password manager, is still better than none. Your first factor can be stolen in more ways than just compromising your machine, for example through data breaches.
So, in fact, the short answer is no.
The answer is only yes if the question is “Hibernating and booting into another OS and modifying the same partition externally: will my filesystems be corrupted?”.