They might have fixed this. They switched to using plaid for external accounts this year, and I was able to add several banks which had 2FA earlier today.

I ran into this for alliant. Reach out to YNAB support, they adjust your account supposedly to not use Plaid for instances like MFA being enabled. It wasn't clear if its an all or nothing deal though for all your accounts to use Plaid or not.

USAA works fine for me. It just asks you to enter the token during login.

EDIT: and I think it migrated to OAuth anyways so no more tokens

It's been said elsewhere but just in case, they recently started using different import provider(s) and many accounts that were broken before now work great, including MFA ones.