Welcome to the Forum and good luck with your reno. My understanding is that as long as the Blueboard is fixed at the appropriate centres there is no structural reason not to fix it horizontally. The main advantage of fixing it vertically is to simplify patching the joins - in single level applications it will also mean no butt joins where the ends of sheets meet with no recess.
In brick veneer houses they put up the frame, put in the window frames and then brick it in - same story for blueboard. As you said, put in the windows then fix and seal the blueboard around them.
If it's worth doing, it's worth overdoing