I mean you don’t have to authenticate your passkey with biometrics, you can use a password.
I guess I’m not really picking up on what the benefit is you’re going for. You already have a What You Have and a What You Know or What You Are, and you want a second What You Also Have thrown in there. I mean, I guess having that as an option couldn’t hurt. but I also don’t think it’s really necessary.
Passkeys are already more secure than what you’re doing now. If what you’re aiming for is for them to be even more secure than that, then that’s an admirable goal. But as of right now they are worth it just for the fact that they’re more secure than existing solutions.
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.