As we prepare for next year's 2FA requirement for active contributors on GitHub, we're making improvements to our two-factor setup UI to encourage best practices and ensure new 2FA users have their authentication factors set up correctly from the start.
We now take an opinionated stance on which second factor you should set up first – you'll no longer be asked to choose between SMS or setting up an authenticator app (known as TOTP), and instead see the TOTP setup screen immediately when first setting up 2FA.
If you wish to use SMS when setting up 2FA, you can switch your authentication method via the new option at the bottom. In the future, you'll also find security keys there as an option for initial setup on supported devices and browsers.
For more information, see "Configuring two-factor authentication".