The reason for this is that FrontBoardServices attempts to use the existing UISceneSession after the update, with the SwiftUI.AppSceneDelegate class, instead of calling application(configurationForConnecting:options:). Since SwiftUI.AppSceneDelegate still exists in the scope, the internal property _configurationNeedsReevaluation on UISceneSession returns true and the app attempts to launch from SwiftUI.AppSceneDelegate.
As far as I can tell, there doesn't seem to be a way to fix this that doesn't involve invoking the private method -[UISceneSession _updateConfiguration:] to force the configuration to use the correct Scene delegate.
Could someone from Apple maybe advise?