Just a followup on this, after a couple days playing with the console, I don't think it is really an issue -- or at least the problem is so small I really couldn't get a good picture to demonstrate it. :)
Basically it's not that the acrylic doesn't lineup, just that it is a smidgen less tight against the mbf (and overlay between) on the bottom edge as opposed to the top edge. Basically if I wanted, I could get my fingernail, or a thin piece of paper under the acrylic, whereas the top edge is completely tight. It seemed more notable at first, and it's possible as I retightened things it just lays down tighter now, or just from having my palms on the control as I play.
Anyway, not an issue. Thanks for getting back to me, I'm enjoying playing games on it.