The 3925 AE shaft never made production. I know it was in the manual but they decided that the stock shaft was light enough already.
The real difference between aftermarket shafts and the AE one are durability. You won't be able to break (most) aftermarket shafts. Downside: (most) aftermarket shafts made of other materials (alum, ti, mag, etc) can and WILL short out your battery if they come in contact with it in a crash. It's a proven fact...that is why AE stuck with the carbon shaft.