You know, I've been wondering about this lately as well. It's also unclear to me how leveling frets using this thing helps:
http://www.stewmac.com/shop/Fretting_suppl...e_Neck_Jig.html
My only guess is that leveling under tensions might account for any twist created under tension. As you point out, you are going to add a slight bow in the neck upon setup. I've done 3 fret levels and had good success doing it just like you. That is, get the neck as staight as possible and then level. I do take a couple of extra passes on the upper frets to impart a bit of a drop near the tongue end. I hope one of the senior members here can enlighten us.
Best Regards,
Mike.