The reason I set them flush is because I want both coils to be putting out an even load (unless there is a deliberate offset in the wind of course). If the screws are out too much then the screw coil will be picking up more signal than the slug coil.
That's kind of what I was imagining when I followed your post earlier in the week - let the pickups do what they want as Tim designed them, see where that gets me. (Having said that, all mine have arrived from BKP with the pole-pieces out further than I would usually go for - I had to screw them in to get them flush).
BTW When I got a chance to reset the Riff Raffs in my Gibson Explorer, the change was stunning, far more of an improvement (for me) than I got with the Mules in a Love Rock.
Haven't had time to fiddle with the MQs too much (the Love Rock's less than a week old, so I'm spending more time with this new "girlfriend"!)