Short version:
I am having a problem with auto layout top layout guide when used in conjunction with custom transition and UINavigationController in iO
In storyboard add another vertical constraint to main view's top. I have the same problem too but adding that constraint help me to avoid manual constraints. See screenshot here link
Other solution is to calculate toVC frame... something like this:
float y = toVC.navigationController.navigationBar.frame.origin.y + toVC.navigationController.navigationBar.frame.size.height;
toVC.view.frame = CGRectMake(0, y, toVC.view.frame.size.width, toVC.view.frame.size.height - y);
Let me know if you have found a better solution. I have been struggling with this issue as well and I came up with previous ideas.