Opinions are varied. Setian practitioners within and without the ToS generally view Apep as a manifestation of mindless natural process. So while Set posses chaotic qualities (moreover he is an agent of chaos in relation to whoever or whatever process he is imposing his will upon) he is not chaos itself, nor is he order. Apep displays a similar apathy towards humanity. He just is, doesn't give a shit about us. Thus as Set-Horus facing Apep down as he is about to swallow the sun, Set, the isolate intelligence, the outsider, the individual, the victor, the fighter, the unification of his own passions, faces an uncaring world intent on swallowing his light/life. He must kill it to continue to experience time.
Setamontet is likely more qualified to provide a more accurate ToS explination, these are of my own revelation from my own work.