Re: cant get it lined up
VTAC barrel nuts can be the same way. With them, there are little teeth that stick out on the barrel nut that you can grind off once you are tight to allow the gas tube through, it kind of looks like a gear with the tube running through the valleys. If the YHM is a circular barrel nut with holes through, you could cut the web between the two closest holes with a dremel and a small cutter or a small round file (you would never see it when it's on). You would have to be careful, but I personally would not loosen it too much to line holes, and I wouldn't over torque it with the chance of twisting and damaging the upper.
I like to see adequate clearance. I don't like any tension on the gas tube.