because an entire species spanning half the galaxy equals one dude and his army
The Covenant Schism didn't help them.
Covies are very, very incompetent. That is abundantly clear. Which is what happens when political leadership dictates military strategy; IIRC the Prophets protracted the war in order to secure their own power (and presumably to prepare for the Schism, so near the end of the war the Covies weren't even using all their assets (namely Brutes), so not quite their prime there).
Presumably, Atriox warband is far smaller than human sphere, and far more mobile. Assuming Atriox fought with hit and run attacks, basically guerrilla warfare, eliminating him would be very difficult, especially while fighting humans at the same time. Plus Atriox should logically have Covie's tech helping him, like, if he had access to those stealth pylons Covies used on Reach, finding him would be even more difficult.
Of course, this would not make Atriox a military genius, rather he'd just be lucky. Wars are usually lost by losers, not won by winners (meaning, the loser makes more tactical and strategic mistakes).
That said, my assumption is correct, characterizing Atriox as a massive threat would be an overstatement. But overselling an enemy is not uncommon in fiction, good guys tend to win no matter what... Halo is pretty guilty of this already though.