I am not a church-going type, but that doesn't mean there aren't any things in life to be taken on the basis of Faith.
Or, you could also think of it as a sort of natural Law ... that The Old Course is the Constitution, which establishes a set of precedents for the game that should never be overturned.
In a very real sense, The Old Course and perhaps a few other seminal links are the foundation of our collective understanding of golf. To apply OUR modern understanding of golf to The Old Course and find IT flawed, is silly. OUR understanding of golf is always going to be limited. By contrast, The Old Course has stood for hundreds of years, sorting out players hitting featheries to hand-cut holes, down to the most recent Open Championship. It has seen way more than we'll ever see, and it still manages to assert its relevance, as much as we've tried to screw up the game we play over it. If you think you are smarter than The Old Course, you need to think some more.
[Let's just take a simple example. There are plenty of genius Americans who go to St. Andrews and think it outrageous that a road and the former railway line and the o.b. sheds are all factors in playing the golf course. To them, such features should never be a part of golf. How do we know they're wrong? Only because they have existed in play at St. Andrews for all time. Without that precedent, such features would be eliminated from the game by people who don't understand it.]
I DO understand that The Old Course has been modified over the years. You can debate those modifications if you want. Most of the significant changes were made more than 100 years ago, so I am content to call those an integral part of the course by now. I have Scott's book, but I don't like to read it, because what he is saying is that The Old Course was changed in the past and could be changed again. I believe that changing it would be tantamount to the Soviets trying to erase history and religion, so that we have nothing left that we know is true, and we'll have to believe what the governing bodies tell us.
The other thing I understand, which you guys apparently don't, is that even in my own minimalist designs [nearly all of which require more "construction" than most people imagine], often the very best parts are things where I didn't do ANYTHING significant ... they were features of the ground which spoke to me, and caused me to design a golf hole around them. We can call that God, or we can call it Nature, but to me those parts are beyond criticism ... you can say that I didn't use it well, but insisting that it should be taken out is missing the very point of golf architecture.
The Old Course at St. Andrews is full of such features, which were not constructed by men, and which aren't like anything man has ever constructed since, which make it a "one-off" as Sean says.