Well, Comey and his 150 agents must have missed something. When the private server story first broke it was revealed that Hillary had used multiple email addresses on the clintonmail domain.
IIRC, it was in the IG report that said she was the only SOS to use a private email exclusively, and that if it had been asked, permission would not have been given. That couldn’t have been too hard for them to find if the IG had it figured out.