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.
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.