I also use a jig that gives varying lengths, but some of the tag ends still show (not all, but there always seems to be a couple are too long to hide in the twist). If one of the ends is a bit too long to be hidden in the twisting or after some use they start to show, then is when I use the fingernail clippers and wax the ends well.
Chad Weaver uses a method making a flemish twist by using an endless loop jig (in the DVD "Doin' the Twist"). All the ends come out the same length as he twists, but he alternately pulls them tight and cuts them off as he is twisting the loops, and it makes his strings look really nice.
RonP