If the google or microsoft TOTP app is spyware, I have bigger problems.
I don't see what's dumb about them either.
- they involve storing secrets on a readable filesystem
- are tied to a particular instance of a filesystem, not actually tied to a piece of hardware, which fails the "something you have" part of 2FA
- either (a) fail if you reinstall your OS, OR (b) need to transmit secrets to Google and Microsoft to allow you to reinstall the OS, both bad
With Yubikey TOTP you cannot read back the secret, the hardware itself doesn't provide an interface to do that.
For apps that do allow export/transfer, it's up to the user if they want to keep the secret safe. But really at some point it's up to the user no matter what method or hardware you use.
And since most sites don't have an easy way to have multiple tokens, allowing export/transfer also reduces the temptation to insecurely store a copy of enrollment QR codes.