Sure, it would have marks on the phone where it was dropped, it will always show along the sides of the phone where the destructive hit was if it wasn't in the box, there is no way around that. And if it indeed was in the box when it was already broken as the dude says, then there shouldn't be any marks on the phone as the box would have taken the hit or that it was broken when packed.
I fail to see why apple would pack the phone as they did if it wasn't secure inside the box when shipped though if it wasn't obvious damage to the box (which the OP would have noted on before he posted this thread but obviously not)..
But i guess the OP should be safe to get a new phone so i have no idea why he even makes a thread about it before he has done anything about it. I guess he's trying to figure out ways to go around it and that's why he's asking us before hand and blames that he can't contact the apple store. And honestly i don't wanna share all those little things that makes the apple store find out how to determine on how the damage may have occurred if this is a try to get a replacement after one was the fault of the damage..
It doesn't sound logical that he/she would receive the iPhone at night time when the apple support is closed either..
BUT, there is a BUT, i will not insult the OP by saying that he's lying. But i won't believe it either, hence i asked for pics or it didn't happen. If it is the way he tells us, he should have no problem taking pics of the phone and the box and share them with us!