the most accepted theory is that in the alt/purgatory/perfect world the island was under water because thats how the Losties would have imagined it. Yet in one of the alt/purgatory scenes, Ben and his father talk about how they were on the island...
Plot hole much?
That's a good point. I guess it could be explanied by Ben and his dad having their own "memory flash" moment, without needing prompting by Desmond, but then that doesn't explain why Ben doesn't recognise Desmond or Locke in the alt world in the scenes we see them together. If he'd got his memories back he would know who they are, and presumably know it was purgatory.
I also think the whole "Let's be nice to Ben" thing is ridiculous myself. The guy systematically wiped out nearly everyone he came across and was an utter **** most of the time, but all it needs is a smaltzy "I'm sorry John", and everything is hunky dory.