Jerry,
There would be lots and lots and lots that would be different.
Just for the example you cited -- I had the rare privilege of walking Bill's routing at Sand Hills with Jim Urbina just before they started cinstruction of the course. The greens and fairways were all flagged out, and there were 12 or 13 greens out of 18 which were just laying there ready to be grasses. But the 8th green was not one of those. It was at the end of a valley, and the green site was in a low spot, well below the current green, and neither Jimnor I had any idea what Bill was going to do there. What he did was core out all those bunkers around the back, and use that fill to lift up the green, and then dig his little central bunker into the fill pad. I never saw that coming ... but it is sort of the same way we built the 7th green at Ballyneal years later.
Still, I will go back to my original point. The routing determines the golf holes. If we wind up with substantially different routings, then our two courses will be nowhere near the same.