For the new yubi keys with fido support I would recommend disabling OTP it massively improved the user experience for me., in difference to TOTP OTP has done fundamental problems.
And fit reasons not affecting many people OTP is implemented by pretending to be a keyboard which is just anoying in many cases.<p>But all other operation modes (FIDO,FIDO-U2F,PIV, OpenPGP) do not have that problem.<p>So when possible I use password manager + FIDO(-U2F), where no it's password manager + TOTP using the yubikey (I plug the USB-c yubikey into my phone accessing the keys TOTP functionality through the authenticator app).