Not being smart, but if it were mine, I would put on a chrome lifter block cover to hide it. I would have done what you already did and have the dealer and MOCO make note of it.
If you were unfortunate enough to have oil leaks on the jugs on the other side, I would then have it took care of then. Otherwise, I would run it with the chrome lifter block cover for the life of the bike.
I would not let the dealer remove my engine, tear it down, put back together and reinstall. The chances of that getting done with no problems is slim.
It's your bike, do what makes you feel best.
Somebody with a lifter block cover will have to let him know if it will cover all the area to the timing cover.