It turns out the problem was not my git config, but instead Git Credential Manager.

I had Git Credential Manager configured for my credential helper. It turns out somehow I had two accounts in the git credential manager. I listed my accounts via git-credential-manager.exe github list and removed the extra account via git-credential-manager.exe github logout <bad-account>. For example, the account I didn't want was "almenon" so I ran git-credential-manager.exe github logout almenon.

After that the popup went away 🎉