I agree that the Attractiveness point value, at least, seems a little disproportionate, but I think I followed the core book's Attractiveness entry precisely. At -5, "people will be taken aback", and both super mutants and ghouls are ugly enough to outright cause revulsion and fear. "Beings with inhuman features can have levels as low as -10." -6 seemed appropriate - both ghouls and super mutants are always more hideously ugly than any human (human-looking human, anyway).
I had the impression that the revulsion of humans in confrontation with the supermutants is more like a trained reaction - and the quite normal fear when you meet a 2.2 m brute who can rip of your head without many problems.
Ghouls look dead though, and that is normally a good reason for disgust. I also think that Ghouls are uglier than Muties.

I'm pretty sure that Attractiveness is intended to be either objective or measured against humans, and it definitely makes sense to me that super mutants and ghouls would get penalties to interacting with humans.
Isn't that already covered through the minority drawback?

I mean that according to Dungeons and Zombies, Orcs gain a 2 point attractiveness drawback - six points would be three times as ugly ass Orcs. (On the other hand, minotaurs have no penalty at all. It seems that green skin is uglier than looking like an angry cow.)

I think I will definitely use the drawback you came up with. I might make it a 2-point one with a -2 penalty, because I think I'd like to make it significant. Super mutants should have a hard time using the tools and small arms of humans.
The inconvenience and part time role as a comic relief character (and again the supermutant walked against the door frame alone is worth one point of a drawback in a game where inappropriate jokes are worth one as well.

Where's Natural Toughness from?
I thought it is in every Unisystem Core book, but it seem to have mysteriously disappeared from AFMBE. Natural toughness is a 2 point physical quality that gives the character 4 points of armor against blunt weapons like fists or clubs. A more focused form of damage resistance.