I've never done it, and never had a reason to. I'm not saying there isn't a reason to, just that I haven't run into such a reason personally.
One school of thought about this process is that sometimes the anodizing on the face of the upper is uneven or excessively thick, which can prevent getting a barrel nut on the upper with acceptable torque. Lapping the face of the upper evens that front surface, allowing easier and more consistent contact between the rear of the barrel flange and the upper, and allowing for more consistent torquing.
Another school of thought is that truing the face of the upper allows for a more exact fit between the barrel and the upper, which is supposed to help get the barrel more precisely centered. This is probably how Big-Bore is getting his barrels installed with well centered sights, and might potentially help with a precision build.
Since I've never had an upper that I couldn't get a good barrel installation with, I don't think the "uneven finish" theory applies to more than a bare handful of uppers. And the conservative technician side of me says "why remove ANY material when a 'hard to torque' barrel nut issue can be fixed by simply changing out the barrel nut?" If I had issues with my sights needing a LOT of windage or elevation adjustment, I might consider tearing down the upper and lapping the front, just to see if it makes any difference. Further, I might also lap an upper that I was using for a precision barrel build, merely to ensure that I had minimized all of the tolerances I could have any affect on.