I'm not against putting at least some long par 4's into a headwind and short ones downwind. It puts them on the proverbial "edge of par" and tends to stretch out club selections and make long par 4's long again for better players.
Its possible to have a nice variety of hole length, but by putting the short ones into the wind and long ones downwind, have most holes play with, say, driver six iron despite their varying lengths.
Ken's post is more along the lines of what I think it means to design features for the prevailing wind. In the par 3 he describes, I would make sure there was a fw bail out left.
And, as I have written before, I tend to align targets with the wind to encourage certain shots. However, since its prevailing, not guaranteed constant, wind, and I try to fit the land, too, I usually end up with a majority of, but not all greens and fw so aligned. I think thats good, because a course can play harder in off winds, but it shouldn't be impossible.
Of course, the lesser and more variable the wind, the less I worry about green angles, etc. And, the greater the wind speed, the more room I give overall, as suggested. There is the story about TPC that Pete was going to leave forced carries from the back tees of over 200 yards on downwind holes. Somewhere early in the life of the design, a strong counter wind came up and some Tour Pros found they couldn't even carry it 200!