Need NSA Expert

[Bandit]

It's late and have to be back at the ball park early. But I ran into something yesterday I simply can't believe in the NSA rule book or in it's local interpretation. Local NSA is claiming that it is ok to skip a batter when it involves the courtesy runner. I believe local interpretation is combining or mixing 2 different rules.
With the way NSA allows for courtesy runners it is possible that you could end up with the courtesy runner on base when her position in the line-up coming up to bat.
I believe that the rule allows or states that the pitcher of catcher shall return to the base to run for themselves and the batter takes her proper turn at bat.
Local NSA is using a rule listed under the "batting" section to justify leaving the courtesy runner on base and simply "skip" her turn at bat and move on.
My belief or thought is that the skipping of a batter is involved when a batter has batter out of order and a legal pitch has been delivered to the next batter thus making her the proper batter and skipping the player that should have batted.
Has anyone run into this? Is this true? Local official claims "skipping" a batter does not "change" the batting order. Not quite sure how this is possible. Skipping is changing, personally.