History, mostly. Ten years ago 2FA wasn't really a thing for most sites. We built an "alternative login" system, where you could create secondary passwords for your account and optionally set that password to be a "restricted" login. This was when using FastMail on untrusted machines (eg public libraries) was not at all uncommon, and HTTPS and even cookie-based login wasn't widespread and being able to create a throwaway password was very useful!
Over time we added paper-based OTP, Yubikey, SMS and so on but at its core its still just for secondary passwords.
We have started work on a rewriting the whole way this system works, which will work like more "conventional" 2FA systems, and will allow a second-factor on the master password. We're expecting it to be available later this year.