I just built a rifle and I am using an ARMS #40A2 flip up rear sight and a CMMG/DPMS 16" Pre-Ban upper.  

Q1:
I noticed the rear of it sits OFF the flat part above the charging handle.  Isn't it supposed to fit flush against it?

Q2:
It locks itself to the leftmost edge of the flat part above the charging handle.  There is about 1-2mm of space on the right side of it and it's nearly flush with the left.  Is this normal?

I have to adjust my windage to the right like 10-13 clicks to get it centered with my laser bore sighter.  Any input is greatly appreciated.

Q1  The dovetail rails are the most accurate attachment points, much like machinist V blocks to assure alighnment, the flat top is not.
Q2  HUH? Windage is there on all sights to correct where the barrel may be other than in perfect alighnment to the receiver. A bore sighter is only good for aprox. not for final zero, go to a range and find out where the gun realy wants to shoot, the make your windage and elivation adjustments. If you have to use up all or most of your windage adjustment, blame the barrel alighnment, not any rear sight that is telling you that you have a barrel/rec. problem. Some weapons will allow you to have the peep sight dead in the center, but not too many.
Good shootin, Jack

I have the same sight on the same upper!

Mine is like yours and there is a space between the flat top.  I believe 3rdtk answered why this is.

When I dialed in my ARMS 40A BUIS for IBZ I was within a couple of windage clicks to zero.  As always YMMV! [:D]