Yes, It is a poorly designed cover. There should have been a circular opening above the 6550 tube. ARC says that the poly cover sounds better than metal. I have a Ref 5se with both metal and poly covers. I can't hear any difference. ARC has had so many problems with the poly covers that you would think they would do something. The new Ref 6 also has a poly cover.
Complain to your dealer. ARC will send him a replacement metal cover. I would do it soon as I have heard that ARC may not get more metal covers when they run out.
I am a bit concerned about the heat build up inside the case when using either cover. I keep my Ref 5se in a rack and don't a cover. It has much better ventilation this way.