The only issue I have with pieced backings when using a Long Arm is that you really want to mount the quilt so the seams run the same direction as the bars. So if I wanted the stripes to be "vertical" and the seam was also the same direction as the stripes, I'd measure to see if I could mount the quilt sideways instead of lengthwise. This could be a problem if you are going to use a panto or computer design, but if you are doing MFQ then it probably won't matter.
When I quilted my Gypsy Wife, I deliberately mounted it sideways so I could easily quilt motifs to enhance the striped nature of the piecing.