Let me phone up the Carpentry instructor at Red River College in Winnipeg. I know that when they measure window openings, they measure across the top, middle and bottom, and use the smallest dimension. Similarily, they measure height on the left side, right side and middle and, again, use the smallest dimension. And, since the bottom of the window frame is sloped downward to allow for rain water drainage off the sill, all of these dimensions need to be taken in the plane where the inside surface of the glass will be. And, once you have the height and width of the opening, you need to allow for 1/8 to 3/16 of space all around the glass within that opening, so you'd deduct 1/4 inch from both dimensions to get the glass size.
But, I also know that they measure the diagonals because the opening may not be rectangular. It may be a parallelogram like the one shown below. This is the kind of shape you get if you have settling in your house and one side of a wall settles more than the other. (The preceding height and width measurements won't distinguish between a rectangle and a parallelogram, but the diagonal measurements will.)
But, what they do with the diagonal dimensions is something I don't know. There has to be a rule of thumb by which the height and width of the glass is reduced because of any measured difference in the diagonals.
I feel a bit embarrassed here. I always install sealed units myself in my own building, but the window company always comes out to measure the opening. So, I'm much more knowledgable about installing the sealed unit in the opening once you've got it in the back seat of your car.
Lemme phone Red River College School of Carpentry and find out exactly what they do with the diagonal dimensions once they know them.