You must have used some weird other SSO systems is the only explanation I have.
GitHub has all the normal SSO stuff as anything else we use, but on top of the GitHub-specific account login. Everywhere else I just log in via SSO, in GitHub I log in first to GitHub (with its own MFA) and then the same SSO step as anywhere else.
I've never had to log in to Github as part of my daily flow. Only once to set up a new computer. Are you logging in using an incognito window or something?