The rubber disk in the pictures is there to seal the point where the antenna base meets the roof. It should not be under the NMO mount, it should sit around the outside. I may be removed to address the spacing issue, but if the right mount is installed correctly, then this should not be an issue. The single rubber O-ring, not to be confused with the flat seal around the outside, should be the only thing under the outer threaded ring of the mount.
You can eliminate the outer flat seal, but that may cause water intrusion up through the threads where the antenna base mates to the mount. Getting water under there can cause a whole mess of issues and should be avoided if at all possible. I know there are those that will fight to the death to disagree with that, but I've personally diagnosed issues where a failed RF output was directly traced to a corroded NMO mount due to missing or failed seals. When a 100 watt MCS2000 is only putting out 1.5 watts, you go looking for the cause.
