Do this. Take a sheet of paper, mark a rectangle on it and in the rectangle, draw something that is asymmetrical such as a box shaded on one side. Also draw some spots on it like dust donuts. This is an image pointing East. Now turn it 180 degrees and that's the image pointing west. All you did was turn the image upside down but it's in the exact same objective orientation no matter how you turn it.

now to to your point, when you calibrate your lights, the ones from the west are upside down compared to the east ones and that applies to both the lights and the flats. You now have two choices. You can either use the east flats with the east lights and vice versa or you can flip both the west flats and lights so everything is in the same orientation. But just like the lights, so long as you orient the flats the same way, they can all be combined into one flat master.

That said, the first way is the much better choice, otherwise you start messing with your darks and your head will really be spinning.