Longarmers prefer horizontal seams because a vertical seam has more thickness at the seam than the rest of the backing, and that spot will get thicker and more distorted with every roll. A horizontal seam will cause that same bump all the way across the quilt and only on one roll. It won't distort further.
And honestly, in the grand scheme of things, do it the way that makes the most sense to you and the most economical. No quilt police here.