How would it be fixed?
Some data on a pitcher is put into the rating system. What comes out is ratings on how many pitches he has and how good they are which is intended to result in performance matching real life even though its all made up. Same with holding runners. A guy gets a reduced rating for holding runners and a little better rating on his curve ball and it all evens out.
I don't see any reason to pick on holding runners being based on nothing when the reality is much of a pitcher's detail ratings are based on nothing. They're all a set of numbers that produce the desired performance result. The numbers can be modified infinitely and as long as the proportions are right the result is the same.
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