I generally leave a 5mm on top, especially if the stem has cutouts in the part that contacts the steerer tube, like a Thomson. Looking at pics on the internet, your Aeffect stem may or may not as well.
If it were a short, solid stem with full-contact I might chop it flush, and stick a 2mm spacer to allow for the preload cap.
Or are you meaning from the upper headset race to the stem?
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