1. "Seriously, by virtue of size Atlas is far stronger than Ganondorf is." What makes you think he couldn't overpower him? He easily overpowered Cronos.
2. Yes, I am talking to you. I am above you 🙂
3. True, he hasn't appeared to be straining, but he's only been there for 10-20 years. And for a titan, i'm sure that's not too long. Like said, he was still using his back arms, though. I guess we call PIS if Atlas could be held down by chains 😐 If he didn't need "all of his arms" then why didn't he just use the two he had when he got chained in CoO?
5. Last I checked, the subject wasn't that Ganon was stronger than Atlas.