I am interested in the grain orientation aspect of the above thread.
I have the Incra LS Positioner, so the jig setup question is not strictly relevant to my question. I have used the LS once for a small box using box joints where I used 1/4" Baltic birch plywood (BBP). The BBP grain is relatively plain and uniform and I was focused on simply learning how to use the jig to make the joints, so all I needed to do was avoid the void patches.
However, as I use it more and begin being concerned about grain orientation, I am wondering how to go about maintaining grain orientation. Perhaps this will become self-evident with use, but I am wondering now. With the LS, you can cut boards individually, but typically two or more boards are stacked and cut at the same time. Also, the cuts are made with the boards against the fence and that side of the boards become the reference sides.
For box joints and possibly through dovetails, my first guess is that outside grain surfaces should be facing away from each other. Once the first sides are cut, the pieces are rotated 180º to put the ends that were up, down on the table. This places the "reference" edges on the outside, away from the fence, so it seems to me that the boards need to be rotated another 180º (in a different plane) to put the reference edge against the fence. As said, this seems like it works for box joints and through dovetails. For half-blind dovetails, it seems that does not work, unless the boards are so perfectly centered that the edges will match.
With the regular jigs (like the one in the referenced thread), there are what amount to two "reference" surfaces, the little "side fence" on the right and on the left so when the pair of boards are rotated 180º, the reference surface (edge) of each board is maintained against one of the fences. With the LS system, the only way to accomplish this is if one of the two boards were to be fed into the cutter from the opposite direction, which I'm assuming is not a good idea. Short of doing it this way, my sense is one just has to deal with any mismatch of the reference edges by sanding or other means of making them even.