you ask a lot of good questions! Every quilter is different. Lost always cut the back out and have no trouble. Lots leave it on. It's up to personal preference. If your using the freezer paper method, it won't hurt to cut the back out. You batting and backing will be thick enough that you won't see any colors through the back. If your worried about fray you can always get fray check at your local quilting store and put it around the cut edges. I figure, if I had cut and pieced the quilt top with a bunch of squares, it would have alot more raw edges than that.
Hope this helps, an someone with a bit more experience than me can help more :)