I can't comment on the zero but your scope height is just fine. It's just about impossible to put a scope really low on any AR because of the stock and the top of the rifle being so close, I have no idea what the other poster is talking about.
Here's a pic of my Colt LE6920, considered the closest civilian AR to the M4, with it's Trijicon ACOG, same scope used by the military obviously. As you can see the scope has to sit high enough that when resting your cheek on the stock it lines up with your eye, which is basically impossible with a lower mounted scope. My ACOG sits at the same height as the buis.
Here's my S&W M&P15-22 with it's Nikon Prostaff Rimfire 3-9x40 150 BDC in Burris PEPR mounts.
As you can see your scope location is just fine. I don't remember how close my scope was to zero when I mounted it but if I remember correctly, it was pretty close. You're using a Nikon scope designed for a .22, in Nikon rings, it should be ok. If it seems really off to you perhaps there was something in the scope rings when you mounted it or you have it tightened in a way it's torquing the scope. If you got it zeroed and it shoots accurately and still have a good bit of adjustment in it, then I wouldn't worry about it.
Good looking setup by the way!