Last thing you want is to do is increase a fixed tolerance. Rather, use your finger for ridges. Meaning, if it feels like nothing is raised from the gouge, but smooth across the line, the tolerance gap wont stop the piston between that rise of tolerance.
The quad ring wont be affected being that the quad ring is square over the piston like this ( | | ). Under pressure, the quad is pushed from square and now looks like this ( / / ). Upon release, the quad's memory returns to square ( | | ), which pulls the piston back and away from the disc.
That's why a minor scratch before the quad wont do shit as far as leaking or losing pressure.