I know that atheists can deal with a lot of prejudice from believers about why they are atheists so I would think that atheists would try and justify their beliefs based on the best beliefs and arguments of a religion and not extreme outliers for both, as otherwise it plays to the prejudice.

Really? It don't think it takes an exceptional degree of rationality to reject religion.

I suspect what you mean is that atheists /ought/ to justify their disbelief on stronger grounds than the silliest interpretation of their opponent's beliefs. Which is true, you shouldn't disbelieve that there's a god on the grounds that one branch of one religion told you the royal family were aliens or something - that's just an argument against a specific form of one religion not against god in general.

But I suspect the task would get no easier for religion if it were facing off against more rational individuals, who'd want the strongest form of the weakest premise. (In this case I suspect something like: What you're talking about is really complex/improbable, before we get down to talking about the specifics of any doctrine, where's your evidence that we should entertain a god at all?)

What I am wondering about is why it seems that atheists have complete caricatures of their previous theist beliefs.

Selection bias maybe? You're talking to the atheists who have an emotional investment in debating religion. I'd suspect that those who'd been exposed to the sillier beliefs would have greater investment, and that stronger rationalists would have a lower investment or a higher investment in other pursuits. Or maybe atheists tend to be fairly irrational. shrug