Are you sure that the rear takedown lug is is bottoming out on the lower's shelf? Reason for asking, RRA is known for having a tight fit in this area, not for having a high shelf (at least not that I've heard of). From what I experienced and have heard others have run into is that the width of the opening of the rear shelf area of the RRA is on the lower side (tighter) of spec, while the takedown lug is on the high side.
On mine, it took a good, firm slap to get the upper to seat fully, and after a few open/closings and a couple hundred rounds of firing, it loosens up so that it snaps together. If this is the case, then you really don't have a problem.
Others have taken the approach of removing very little metal from the sides of the lug, while others have suggested taking a file to the lower. Personally, of the 2 options, removing a little from the lower is probably the best option if you are going to go this route. Since the upper fits on your other lowers, I wouldn't bother taking metal off the upper lug.
We are only talking a few thousandths of an inch, so you don't have to take much off in any case.
In my own case, I liked the tight fit, and after a short time, the opening/closing wasn't an issue.