Tom can answer that better since he's got the thing in hand, but the setup shouldn't have changed at all during shipping. It got a lot of time on the setup fixture under tension, so any settling that needed to occur had a chance to do that.
We were originally going to ship it in a hardshell case, but two things got in the way of that. First, there is no hardshell case that will fit that guitar exactly. Second, the size/shape of guitar cases cause all the shippers (UPS, FedEx, USPS, etc.) to hyperventilate and go into mega-profit mode, so I separated the neck/body for shipping. Cuts the cost to less than half. Plus, it allows for more protective packaging and easier handling. Means the customer has bolt the neck on and string it up at the destination, but there's nothing to that.