The purpose for setting string heights at the nut/zero fret higher than the plane of the frets is to prevent buzzing of the open strings for those with a heavier attack. Those with a lighter attack can have strings set to the plane of the frets.
The difference between an open string that buzzes and one that doesn’t can be one stroke of a file. Not every setup person is willing to live on that edge and file nut slots that low. Many will leave themselves a cushion. Many players can’t distinguish that difference.
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