We can ignore the part about the individual start channels because that's something that went back to a much earlier set up when I had gaps which I've fixed since then.
The problem is with a conventional setup letting xlights do the zigzagging instead of the controller, sequencing at the Strand level has some strings behaving in the opposite direction.
With my custom set up showing 36 strings instead of 12 like I actually have it shows overlaps on the visualize controller.
I was hoping that adding a zigzag to the controller connection will allow xlights to behave correctly at the Strand level while allowing me to better match my physical layout.