It's hard to tell from the picture but the armwand looks duller than the matte silver finish on the RB-700.
Regarding the 3 holes in the plinth. When Rega pre-drills the holes for the screws, they don't countersink the holes so what happens is they install the arm and tighten the 3 screws. Everything is fine until you remove the arm and 3 screws for the first time and the holes expand at the very top and basically raise up.
I always countersink the 3 holes but I have the tools, you probably don't, but you could just take a larger size drill and spin it by hand to remove the raised area around the hole. That's my recommendation to fix your problem. After you do that, the arm will sit flush.
BTW, respectfully, you should post this on a new thread.