as with any magnetic pickup in any use, gap can be critical. from the factory, the gap on the pickup coils is probably 40-50 thou.. dropping it to 20 seems to be the sweet spot.
I imagine it could change the timing a small amount (degree or 2 max), and possibly the spark duration (if the CDI does multiple sparks per ignition cycle, which I dont think it does). since the insides of the CDI are kinda mystical, we dont really know when the spark is generated during the pulse received from the pickup. it could be leading edge, 'centered/peak' or on trailing edge. the closer the coil is to the magnet, the longer in duration the pulse, and stronger. I believe its the stronger pulse that cures the hot start problems that are not cured by AGM batteries.
when I set mine, I used a metal feeler gauge, of course it stuck to the magnet, but I put the feeler gauge between the pickup and the magnet and set the coil down to the feeler gauge. then I removed the feeler gauge and verified the coil didnt move once I pulled the gauge.
if your off a couple thou I doubt it will make a difference.