They also make no allowance for Clinton being attacked in the general - we all know she was the gOP's preferred opponent, hence Operation Chaos. I still think she would have won - but wouldn't speculate on the margin.
What the exit polls cannot do is factor in the amazing Obama ground game, so influential in states like Indiana. I don't believe Hillary would have had the organization to get as many voters to the polls.
VP choice is about the fit between candidates, and ability to work together. If Obama had chosen HRC, the narrative from here to Nov would be all about their relationship, looking for fault lines, and using past quotes to divide. It would be a huge distraction.