Brad,
That's exactly correct.
The original nine holes started where the wacky putting green exists, which is where the original golf shop was located.
The first nine progression was the present holes 5, 6, 17, 18, 1, then the abandoned par three, then 2, 3, 4 back up to the putting green.
The 3rd hole is amazingly weird, as you mentioned and I've never understood the clubs contention that Ross was somehow involved.
What's more, in the Flynn archives that Wayne Morrison has there is both a routing plan and individual hole drawings for today's holes 7 through 16. Interestingly, the routing plan makes accommodations for cottages to be built between each of the holes, something that was never actually done.
The drawings are in the same handwriting as those of Lancaster CC, and others of Flynn.
I still haven't the slightest idea where Ross plays into all of this, and why the club contends that he does. It may be that he stopped over during his work at nearby Buck Hill in the 1918-1920 timeframe, but we do know for certain that the somewhat bizarre first nine holes were on the ground by 1912 (way before then) and that the second nine represented in the Flynn drawings was there by 1920.