I think it's genuine on both sides. Abed doesn't seem to have any trouble experiencing emotions, he just doesn't express them as much as other people. He's more confused by some arbitrary social rules, like when it's okay to call out bitches, and when it's not. As he explained to Jeff, he understands life (and can distinguish it clearly from tv), but he prefers tv because it's structured and obeys a clear set of rules. Troy's unwavering loyalty is a huge assuring constant for Abed, plus they just like many of the same things, like video games, the Kickpuncher franchise, making friends with war criminals, beatboxing, silly morning show bits, and of course crumping.