I am all in for adjusting the velocity. (Trajectory Validation) As long as you know for sure all
other data is spot on. And yes especially the zero. What ever you are off on the zero will carry through on out. Off 1 moa (1.047") at 100 will be off 1 moa (10.47") at 1000. One thing I have learned since buying some higher end chronographs is, if you trust them they will encourage you to find the real problem. Changing the muzzle velocity might get you on to a certain distance, but if that was not the real problem it will show up again later down range at longer distances. Many shooters seldom check scope tracking to be true to the .25 moa. And no, not that box test at 100. It will not tell you squat, other than the knobs do work. You may not be able to detect a turret that is tracking 1.05 moa, an error of (.043") instead of 1.0 moa at 100, but trust me you will at 1500 yards where it turns into almost 2 moa or 31.5".
You might be surprised how many scopes are just a little to either side of a true moa.
I just wanted to point out the velocity could fix it at some distances, but if the true problem is something else it is no more than a band-aid waiting to fall off.