Apologies for the ambiguity of the question; I'll try to explain clearer here.
The Problem
I have some code in AppDelegate.swift that performs conditional navigation; if the user is signed in (and therefore currentUser is not nil), the app will start in View, a View Controller in the Main storyboard. Else, if the user isn't signed in, the app will start in Welcome, a View Controller in an Auth storyboard.
The following is my code from AppDelegate.swift, ViewController.swift (which is View), and WelcomeViewController.
Note:
Viewis the Storyboard ID I set forViewController;Welcomeis the Storyboard ID I set forWelcomeViewController.
AppDelegate.swift
import UIKit
import Firebase
@UIApplicationMain
class AppDelegate: UIResponder, UIApplicationDelegate {
    var window: UIWindow?
    func application(_ application: UIApplication, didFinishLaunchingWithOptions launchOptions: [UIApplication.LaunchOptionsKey: Any]?) -> Bool {
        // Configures the Firebase library.
        FirebaseApp.configure()
        // Performs conditional navigation on the condition of currentUser's status.
        self.window = UIWindow(frame: UIScreen.main.bounds)
        let user = Auth.auth().currentUser
        if user != nil {
            let storyboard = UIStoryboard(name: "Main", bundle: nil)
            let rootViewController = storyboard.instantiateViewController(identifier: "View")
            window?.rootViewController = rootViewController
            UIView.animate(withDuration: 0.5) {
                self.window?.makeKeyAndVisible()
            }
        } else {
            let storyboard = UIStoryboard(name: "Auth", bundle: nil)
            let rootViewController = storyboard.instantiateViewController(identifier: "Welcome")
            window?.rootViewController = rootViewController
            UIView.animate(withDuration: 0.5) {
                self.window?.makeKeyAndVisible()
            }
        }
        return true
    }
}
ViewController.swift
import UIKit
class ViewController: UIViewController {
    override func viewDidLoad() {
        super.viewDidLoad()
        // Do any additional setup after loading the view.
        print("ViewController presented.")
    }
}
WelcomeViewController.swift
import UIKit
class WelcomeViewController: UIViewController {
    override func viewDidLoad() {
        super.viewDidLoad()
        // Do any additional setup after loading the view.
        print("WelcomeViewController presented.")
    }
}
Expectations
The app is freshly installed on the Simulator, and therefore there should be no currentUser (and upon debugging, proves to be true). Therefore, I'd expect to see this as the output in the Console:
WelcomeViewController presented.
Instead, this shows up in the Console:
WelcomeViewController presented.
ViewController presented.
Attempts
So far, I thought that the problem might have arised from the fact that Main storyboard is the default Storyboard set since the creation of the project. Therefore, I tried unchecking the 'Initial View Controller' checkbox for the two View Controllers. Just like I'd expected, the following appears instead:
WelcomeViewController presented.
2020-06-20 11:39:38.724658+0800 AppName[11439:237509] [WindowScene] Failed to instantiate the default view controller for UIMainStoryboardFile 'Main' - perhaps the designated entry point is not set?
What should I do to make sure that ViewController doesn't appear and replace WelcomeViewController? All help is appreciated, thanks!
 
    