In my experience it is perfectly fine to add another UIWindow
on top of the default one.
I also do not think that this is like taking control of the app at a low level. If I consider that the iOS SDK is closely related to the MacOS SDK, I tend to think that multiple window are perfectly supported at a higher level of abstraction: it is only that on iOS they are not so necessary or useful (generally speaking, apart from specific cases).
Digging a bit on the web, I found this interesting discussion on S.O.
Hope it helps.