I assembled a Bushmaster A1 upper to a BM superlight 16" barrel and it shot low and  right even at 50 yd with the adjustments maxed out on the sights.  I did not overtorque the barrel and even when I disassembled it, it boresighted the same way with the barrel in the receiver without the barrel nut on (its a very tight fit).  I know I can buy a tool to true the face of the receiver, but I just called Bushmaster and they said they would fix it.  

Am I better off just letting them deal with it or fixing it myself?

That really depends on how fast you want it done and whether you are willing to give the effort to fix it yourself. I'm sure Bushmaster would be able to make it right if it's a major flaw, when you try it yourself and find that you need to do more than simply straighten out the interface, you'll probably wish you'd sent it to them in the first instance. If the index pin is improperly placed they'd replace the barrel, if you do it, you'd replace the barrel, or get real crazy with a file.   It's also low and not simply left or right, is the front sight post maxed too?

yes, the front sight post is just about maxed out.

You did lower the front sight to raise the point of impact?

Yes