An aside: I wonder if the question would've garnered more responses/greater detail with a different hypothetical architect, eg Colt or Fowler or CBM, or anachronistically, Jeff B or Tom D or Jack N.
Sorry, been busy. Of course impossible to answer, but my guess is it wouldn't be much different than the other dozen times I have worked with a tour pro (or in this case, champion amateur golfer). I think we would have had an initial meeting discussing some parameters, like his love of St. Andrews and the idea of implementing, but not copying hole concepts.
I would then bring back a few routings for Bobby to review, he would make a few suggestions, we would refine it to the final, put out the centerline stakes and go from there. I would probably sketch out some bunkering, etc., for him to review. Again, he would "edit" and then construction might start. Not sure if he would be at every site visit I made, but probably a few more than normal (i.e., Colbert at Colbert Hills, his baby, and over a dozen vs. 1-2 for publicity purposes).
As to the routing itself, I have told this story, and don't even think its probably true, but I met a man at a Singapore golf show 30 years ago claiming to be a grand nephew or something. According to him, family legend and a few letters show that Mac argued against using the farmhouse as clubhouse, thinking it forced too much an up and down routing. Of course, I have no proof and he never produced the letters, for me at least.
I will say, I would probably have tried to produce one routing starting somewhere else, just to see how it might work out. Had Jones been able to see the future, he would have known that a Berckman's Place tournament pavilion was going to be built eventually, and put the modest starting shack where it needed to be, golf wise, and then retire to the grander accommodations post round.
But, I have lost jobs pushing alternate clubhouse locations too strongly, so if I had been commissioned later in my career and wanted to stay on the job, I would probably declare, "Best clubhouse location ever!"
and work from there, LOL>