We had originally planned to go all-in on passkeys for ONCE/Campfire, and we built the early authentication system entirely around that. It was not a simple setup! Handling passkeys properly is surprisingly complicated on the backend, but we got it done. Unfortunately, the user experience kinda sucked, so we ended up ripping it all out...
I am very shitty on security (I would not write this reply on a post on the cybersecurity community), and I resisted MFA for several years as being too annoying having to login to mail/SMS. After finding open source apps supporting TOTP, I feel better about it and I manually do the syncing by just transferring the secrets between my devices offline.
Passkeys are another foreign thing that I think I will get used to eventually, but for now there are too many holes in support, too much vendor lock-in (which was my main distaste for MFA, I didn’t want MS or Google Authenticator), and cumbersome (when email and SMS were the only options for MFA, difficulty of portability for passkeys).
So the problems you have with them are already solved, in the exact same ways they were solved for password/MFA. If you let Apple manage everything for you, it doesn’t matter whether you’re using passwords or passkeys, you’re locked in either way. But you always have the option to manage your passkeys manually (just like you’re doing with your TOTP) or using a third party cross-platform solution that allows for passkey import and export.