Have no experience w/the Megas, but have noticed a difference in the thickness of different brands of lowers, and uppers too for that matter.
Since I have lowers made by Colt, Rock River(2),
DPMS, and Bushmaster, I went ahead and measured all of them at the side wall directly over the hammer pin hole. Thickest was Bushie, next Colt and DPMS (only .002 difference), and thinnest were the Rock River jobs.
For me the question isn't safety; it's fit. I really don't want a rifle where the upper edges overhang the lower, though I can live w/a rifle where the lower is a couple of thousanths wider than the upper. With this in mind, one RR lower has a no name upper on it that's about a thousanth wider than that lower on each side (I can live w/that[:D]). The M4gery has a Rock River upper on the DPMS lower. Perfect fit on one side, slight overhang of the lower on the other.
The Colt SP1 is Colt top and bottom, for obvious resons. The M16A1 clone has a Colt upper on the Bushie lower, which overhangs the upper by about .002 on one side, and perfect match on the other. The M16 clone with the Air Force surp Colt upper is a perfect fit on the new Rock River lower.
So, if I see a Mega lower at a show, and I've got a project in mind, I probably will already have an upper for it. I have always built up my top ends first. If what's on the tablr will match up my upper pretty well, fine. If not, move to the next parts guy[:D]