has nothing to do with the "barrel tightness" and doubtful the upper is out of whack. when the barrel nut is tightened it drags on the front of the barrel extension which in turn rotates the barrel in the upper to the point that the aligment pin hits the side of its slot in the upper. this is much more noticeable on carbine barrels due to their shorter sight radius.

you can pull the barrel off the upper and reinstall it while boresighting it (per the TM) or drift the barrel over by applying a no mar ( I prefer rawhide) mallet to the appropriate side of the FSB. The latter is easily done on the range in conjunction with zeroing or can by done in the shop in conjunction with boresighting.

not really, you're not applying any torque to the barrel that way.  even with a mallet you have to make sure the upper doesn't rotate and even then the movement is often small. I've had my rifle drop 6 feet onto a concrete range floor and land squarely on the side of the FSB right after putting a 100 yd zero on it. Picked it up and the zero hadn't moved. You gotta want to move it.

I wouldn't recommend filing the notch in the upper unless you can prove the notch is off center, in that case I would attempt to return the part to the vendor. Changing the location of the notch changes the timing of the barrel extension lugs and can increse bolt wear. You'll also be rotating the gas tube. Correct the faulty part do not fit a good part to make a bad one work.

with the combination of factors at play leading to misalined sights I would point to the barrel as the one part that causes the most alinement issues, there are several more steps in barrel production where an error can be introduced opposed to upper production.

removing metal is always a last option with ARs.

while anything can do wrong, I don't see a lot of danger in bore sighting (as in looking down the bore meaning the bolt carrier is completely removed from the upper) an upper.

Doing it with a laser would be a and obviously live fire is out of the question.

I know of one mid range manufacturer that used to boresights their uppers through the assembly shop window at a white picket fence around a trailer park across the street from the factory. Never had an AD doing that.