Hide switching of storyboards

In my application I have 2 storyboards: Onboarding and Main. When user opens app for a first time - Onboarding storyboard is presented. After that, he presses a button and I show him Main Storyboard with such code:

let storyboard = UIStoryboard(name: "Shop", bundle: nil)
let navigationVc = storyboard.instantiateViewController(withIdentifier: "ShopScreens") as UIViewController
navigationVc.modalPresentationStyle = UIModalPresentationStyle.overCurrentContext
self.present(navigationVc, animated: false, completion: nil)

I wanted to make custom animation, when user switches storyboards. To do so - I've created simple view that I'm presenting on top of everything like this:

UIApplication.shared.keyWindow?.addSubview(self.containerViewForAnimatedView)

And this view is working fine, but only in terms of one Storyboard, it covers everything while app changes screens.

But when I try to switch storyboards - this view gets covered by newly presented storyboard.

I also tried presenting view in such way and brining it to front:

let appDelegate = UIApplication.shared.delegate as! AppDelegate
appDelegate.window?.addSubview(self.containerViewForAnimatedView)

But that din't work as well.

How can I hide switching of storyboards by presenting custom created view during that transition? Would be grateful for any help.

Just played around some with it, no animations or anything special but this will give you the flow that you want:

class ViewController: UIViewController {
    let viiew = UIView.init(frame: UIScreen.main.bounds)

    override func viewDidLoad() {
        super.viewDidLoad()
        view.backgroundColor = .red

        DispatchQueue.main.asyncAfter(deadline: .now() + 3) {
            self.viiew.backgroundColor = .blue
            UIApplication.shared.keyWindowInConnectedScenes?.resignKey()
            UIApplication.shared.keyWindowInConnectedScenes?.addSubview(self.viiew)
            self.viiew.layer.zPosition = 1000
        }

        DispatchQueue.main.asyncAfter(deadline: .now() + 4) {
            let vc = ViewController2()
            UIApplication.shared.keyWindowInConnectedScenes?.rootViewController = vc
            DispatchQueue.main.asyncAfter(deadline: .now() + 4) {
                self.viiew.removeFromSuperview()
            }
        }
    }


}

class ViewController2: UIViewController {

    override func viewDidLoad() {
        super.viewDidLoad()
        view.backgroundColor = .green


    }
}

extension UIApplication {

    var keyWindowInConnectedScenes: UIWindow? {
        return windows.first(where: { $0.isKeyWindow })
    }

}