According to an article written by Darwin shortly after MacKenzie redesigned the course, the biggest changes came on these holes:
4-he created a gap in the crossbunker
5-he moved the green to the right on to a plateau
6-he created a new par-3, with a new green surrounded by bunkers
8-replaced the blind green; he moved the green to the right where it would be visible (Darwin regretted this change).
16-replaced the blind green, he described the new green of being in the shape of gully built into the side of a hill (he preferred the new hole, although he liked the old hole).
17-moved green from behind the dune (Darwin liked the new green, although he thought it was a little too small and boldly contoured when the wind blew)
18-the new hole was a big imporvment over "one of the worst, longest and dullest holes in Europe". Although he did comment that the new green had a slightly plasticine appearance, clearly the work of MacKenzie as opposed to Providence, he thought perhaps time would remedy that. I wonder if Darwin's observation have anything to do with MacKenzie's comments in the Spirit of St. Andrews about the dangers of using plasticine models?
There was no mention of the second hole. If MacKenzie did plan on cutting a gap through the dune, I wonder why it wasn't done while he was making all the other changes. And if that was his plan, I suspect his gap would have looked a little less geometric/symmetrical.