I've heard that pros do this when they find that the dots on the approach are on the wrong board on a given lane. Of course PBA rules are slightly different from USBC rules so it might not be okay for the rest of us. And the bowling center manager could claim that you're defacing the approach and ask you to stop.
As far as being unfair, I don't see anything wrong with it since bowling alleys have plenty of pencils and any one else would be free to make their own mark.
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