Anyone interested in 83 Pace Arrow Tear down and Rebuild?

Yeah, that makes sense. The Kreg jig moves up on thicker stock so that the screw will exit the stock in the center of the edge. That is why your screws are not centered in the piece. You essentially lowered the jig by raising the workpiece so it shifted the hole towards the edge.

BTW, you can get the screws in either head style in any length. Some stores just don't carry the complete collection. But like you said, one the glue sets, it does most of the holding anyway.