Gib - to quote/paraphrase a non-golfing philosopher: Remember, when you stare into the abyss, the abyss stares back into you.
I think many of the decisions that architects make, especially the ones that most reflect their personal styles/ethos, are in large part unconscious, and thus can emerge either as fresh, wonderful new ideas or as notions/preconceptions that have lodged themselves there in the unconscious during years of studying and working on their crafts.
I think the matching nines you mention, the two fives and the two 3s, the par 72 is clearly a framework/assembly of notions and preconceptions that have lodged themselves there, and to such an extent that even architects who think they might be free of them -- who might even believe that they are designing what the site is giving them, and that they are routing a course based solely on the best holes and puzzle they can see/find -- may end up 'unconsciously' using the same framework yet again i.e. may actually "see" the matching nines and two par 5s and two par 3s a side as the best and most interesting use of the site.
(They have been staring into that Par 72 abyss since they first fell in love with gca, and the abyss has stared back into them.)
I think this is what can and most often does happen...unless, unless that is the architect makes a very conscious and very determined and very consistent effort NOT to accept that framework, which is basically a decision not to follow 'what comes naturally/easily' to him, and not to automatically go with his 'first choice'.
That is a tough thing to do, I think, especially if success in the past has given that architect very good reason to feel confident in his easy/natural choices. That's why we don't see it more often from architects, even the very good ones, and why there continue to be so many courses following that same old pattern. IMHO of course
Peter