Actually, the seam being vertical creates problems that result in tucks on the backing - as the quilt is quilted and rolled up together on the take-up bar, the seam is double thick and that builds up over the turns on the bar, making where the seam is very tight and the sides become quite floppy. I prefer my customers to have the longest seams running parallel to my bars so I don't risk floppy sides and tucks. I frequently piece my backs and I just make sure that the seams that are the longest are the ones that I parallel to my rollers. It you are not going to use a longarm to quilt a quilt with a pieced back, the only thing I would think of that may cause a problem is if you have a pinwheel-like block on front and back that happen to line up perfectly to create a little volcano of layers of seams - that will cause the needle to deflect and give you crummy stitches, no matter what you are stitching with.

I usually just make a simple pieced back. I sew 1/2 to 1" seams and quilt my own quilts Usually I join WOF quilt.