Note the "by default". That suggests the FBI isn't interested in spying on smart people. They only want to go after the dolts who cannot be bothered to enable encryption. Mr Comey obviously doesn't think much of his adversaries if he assumes they won't bother trying to hide.
Either that, or they want to spy on the population generally for purposes other than the prevention of crime. Which is it? Does be believe terrorists are not tech savvy, or does he not care about clever terrorists and instead wants to monitor the plebs? I doubt he has any coherent answer beyond beyond 'More data = good'.