Those are good points. I bring up the naturalistic fallacy in my next article on Rand, which is coming out soon. And indeed, the instrumental rationality of egoism might be illusory if such aggressive selfishness ends up making the selfish person a pariah. Rand's point in Atlas Shrugged is that the egoistic industrialists can take care of themselves, so they have nothing to fear from a rebellion of the have-nots. But that's quite a dubious (not to mention obnoxious) myth.