Not quite the only one, Foli also uses his A3 AoE as well. Point being that a lot of champs use abilities for no reason in auto and it will likely stay that way since they've known about it since day 1. I'd recommend finding an alternative solution.

Why does athel use her A2 Aoe on the clan boss when no other champ uses there aoe attacks on the clan boss

Any AOE that has an extra effect: example - athels aoe having increased crit chance - foli having block revive, will MOST LIKELY in most cases be used when available.

If you are doing the clan boss on auto, you are doing things SERIOUSLY wrong.  While the boss' AI is designed to kill you as quickly as possible, the only decent AI that Plarium made is the clan boss, not your champions.  After all, less damage on the boss means more likelihood to spend gems on keys, so more money for Plarium.  They have zero incentive to fix the AI.  You have to do it manually to get it done right.