Many do what you describe, probably because some manager somewhere needs to tick some checkbox.

But GitHub, specifically, allows you to sign in with a passkey. On the sign-in page, there's a "sign in with passkey" link. It activates my 1Password extension, asking if I want to use my passkey. I say yes, and I'm in, I don't type anything. This also works the same way with my YubiKey.