Jim,
I can understand your contention that it shouldn't make a difference in the rankings but I can also tell you that some of what is rated includes presentation, maintenance, and most importantly to this discussion, in the case of Golfweek, the following is one of ten overall criteria;
Integrity of original design:
-extent to which subsequent changes are compatible with the design and enhance the course rather than undermine or weaken it
here's another;
Landscape and tree management:
-extent to which trees and any floral features complements or enhances rather than impose and intrude upon the ground features and playing conditions of the course
I personally think those are really good criteria to look at with classic courses, and although I don't believe PV should necessarily drop from the top (simply because it has more great holes than any other course), I have thought long and hard about it personally.
The next bottle of wine will have you seeing the light.