You could always have a dedicated root user with SSH access use an SSH key - that is how I do it.
Also, AFAIK, you can enable several authentication servers. So, you could use LDAP+TOTP plus Local authentication. In that case, you would have the non-2FA user in the local database. It could be the other way around, but that defeats the use case somehow. And I think if you want Local+TOTP, you cannot discriminate by using another "local" source.
Ah - now I understand. As soon as I create a Local+TOTP server all local users get 2FA activated.