The Distortion has one double thickness center magnet. The triple magnet pickups have one center mag, and two smaller spacer magnets on the sides that are oriented to repel the center. I saw an illustration a while ago of how that directs the magnetic field up and out towards the strings, if I can find it again I will post it. But it's all about that magnetic field. If you had them set up to attract one another, the field would be more compact and wouldn't magnetize the strings as much.
I would guess that two stacked magnets would also create a different field than one double-thickness magnet. And remember that the poles of a pickup magnet are the long edges, so if you're stacking the flat sides in a way that sticks them together, what you've actually got is a N-S magnet laying alongside a S-N magnet, not two magnets stacked end to end.