Mark,
Some of this must be an artifact of how architects route the golf course. William Flynn was pretty unconventional in his routing style. He would route all over the place, up and down hills straight on or on diagonals. He has a number of uphill par 4s and par 5s throughout his portfolio.
Maybe the single course that represents this best is Rolling Green GC in Springfield, PA. Ran thinks this course embodies Flynn's general design principals better than any he has seen. Par 4 uphill holes include 4,8,11,12,15 and 18 (sometimes it plays as a par 5, though it should always be a par 4). Uphill par 5 holes include 9 (620 yards with a steep left to right slope for most of its length),17 and 18 (when it isn't a par 4, which should be never).
TCC, Brookline
Shinnecock Hills
Lancaster
Lehigh
Philadelphia Country
TCC, Pepper Pike
Indian Creek (completely man-made island with elevation rise to 35')
Manufacturers
Huntingdon Valley
Eagles Mere Old and New Courses (New Course had 2 par 4s each with climbs of 120')
and many more have such features.
It must be difficult to tie these in to the routing progression so that the walks are not too severe and the holes flow well in the overall structure with proper balance and degree of difficulty. I think Flynn was a master at this and it is one of the design features that attracted me from the very start.