I don't understand what you mean about Hanso faking the crash? I think the type of fake people are talking about is a cover up crash, not the actual Island arival. I could be wrong.
Well, there are both possibilities for this one. I don't get why Hanso would create a fake crash in the outside world either. I hope the writers really think this one through - it seems odd that ALL the bodies were accounted for - I would think that a plan crash 4 miles deep would result in some bodies not being found.
With Johns dad, you know, it's a magic metaphorical box that brought him there, not by conventional means.
That still doesn't explain how Tom Sawyer got to the island...
I'm fairly certain Ben is the actual ruler of the Island, like a president or something.
I think he's managing the others, but someone else that we haven't met is truly in charge. Remember when he was captured and he confessed that the others were serving a "A great man?" I think of Ben as the plant manager, but there's definitely somebody else running the company.