Set rootViewController of UINavigationController by method other than initWithRootViewController

You can solve this by calling setViewControllers.

Like this:

UINavigationController *navigationController = [[UINavigationController alloc] initWithNavigationBarClass:[MyNavigationBar class] toolbarClass:[UIToolbar class]];

[navigationController setViewControllers:@[yourRootViewController] animated:NO];

Swift version:

let navigationController = UINavigationController(navigationBarClass: MyNavigationBar.self, toolbarClass: UIToolbar.self)

navigationController.setViewControllers([yourRootViewController], animated: false)