Happening since morning, I got rid of Gapps on phone (for privacy concerns) and can't use K-9 Mail anymore, guess I'll have to resort to mobile browsers for email access.
I'm not sure if Google allows using phone notifications first (another 2fa method) and then switching to TOTP, but TOTP isn't allowed as the first choice.
Unless it's for work, why not use a different service or host your own mail server? I'd say setting up a mail server with projects like Mail In A Box is easier than living without GApps.