QWindow has been introduced in Qt 5.0 due to the gui / widgets split. QWidget now lives in its own library (QtWidgets); it was necessary to provide the abstraction of a “toplevel window” for non-widgets based applications, and thus QWindow was created — and lives in QtGui.
There is an entire class of non-widgets based applications: all those using QtQuick2. They don’t use the QtWidget library at all, and as a matter of fact, when using them you’re always somehow using QWindows explicitely (QQuickView inherits from QWindow).
Even when using widgets, top-level QWindows get created for you by the Qt kernel, which also keeps the properties and the flags of such QWindow objects in sync with the corresponding top-level QWidgets. This way you can just deal with widgets like you always did, without knowing about QWindow at all. Existing applications will continue to run as expected, etc. etc.
The only reason (so far) I’ve been using QWindows explicitely is for a very specific use case: to draw pure OpenGL content. This is very easy to achieve (by setting an OpenGL surface type on the window), and avoids you to bring in additional dependencies (QtWidgets, QtOpenGL, etc., which have a cost in terms of library size); it allows to create a OpenGL drawing surface in like 10 lines of code which will work on Linux, Windows, Mac, QNX, “embedded Linux”, and very likely Android and iOS too. From this point of view it acts as a perfect SDL replacement. 🙂