On a large quilt, any seam that runs top to bottom can create a problem with the rolling. Seams running in that direction start to pile up on the roll and can create distortion/tension problems. On large quilts, I believe longarmers request that a backing seam run from side to side so they don't have to deal with that issue. On a small quilt, I think it is not a problem.
You may want to contact your longarmer before incorporating the panel into the back.