I think y’all are talking about different things. Some sites (like google) have direct yubikey support where you plug the key into the device and what you’re talking about isn’t an issue

Other sites don’t have direct support, but allow you to use any authenticator app which is what you’re talking about with using the yubico authenticator app/key combination. Plugging it into a yubico authenticator app on any device will show the codes

Unfortunately I don’t have an answer for a way to protect those other accounts. I guess the hope is that if you lose it, it can’t be tied to your accounts, just the websites themselves

Ive been able to create two on grapheneOS when opening up play store in separate profiles and clicking create account on the log in screen