Just measure the distance between and take a 1/4 inch off. You don't want the glass to touch imo. That way when pressure is on it, it has less of a chance to bust the other piece.
FWIW, I've used both types of silicones in my tank and the one with the mold inhibitor does not cause any issues at all. I know many individuals who have used it before. I believe this to be a myth.