Since SG wraps around QT I dont think setting the flags self.setWindowFlags(QtCore.Qt.WindowStaysOnTopHint) works as expected.
Have a look into SG’s window modality options:
https://developer.shotgridsoftware.com/tk-core/platform.html#engines
Otherwise there was another topic where someone added minimize/maximize buttons to the tk-core dialog wrapper.
Your flags may work there: