That's called a mechanical zero.
It irrelevant to a 100y zero. When you add a scope base with moa, then you move the erector even further out of that mechanical zero.
That said, it's not a requirement to start at a mechanical zero. There's a variety of ways to do it. Some more efficient than others.
If it's a new gun, and a new scope, I like to start at 25 yards on a 1 inch square. I shoot, and move the reticle to the bullet hole a few .1 of a mil high. 1 shot. Second shot I verify is a little high, say the top of the 1 inch square.
I move back to 100 and shoot again, then move the reticle to the shot without moving the rifle. Zero'd.
I've been doing this for a long time, so it's a shortcut I myself can do. I can keep the rifle steady, and I can repeat shots fairly well.
For others who might not have as solid of a foundation and technique, shooting a group and zeroing to the average might be the better way.