I read the same article and found it pretty interesting, as I do pretty much all his articles on course design.
The way I comprehended it is that not every hole has a "NAGS" zone mostly just the poorly designed old style par 5's.
Take an imaginary 900' Par 5. A 450' thrower can essentially throw the same shot twice and be putting. A 300' thrower essentially throws the same 300' shot 3 times and is putting. However the 375'-400' driver throws two identical shots before landing in the "NAGS" zone 100'-150' away. It all comes down to consistency it's much easier, safer, smarter? To throw walk up and throw the same 300' shot 3 times as opposed to throwing the same 350' shot twice and and leaving yourself with 100'-150' upshot.
Another way to look at the "NAGS" zone is what Houck calls "Dumb" Holes. The par 3's that are just out of birdie range for most people but short enough that only a mistake costs you par. The "NAGS" zone is exactly such just out of birdie range, but short enough that only a mistake on your part will cost you par.
He goes on to encourage Par 5's designed to play like 3 individual holes from teebox to first landing zone, first landing zone to the second LZ, the second LZ to pin. Also saying that it should be the second LZ to the pin that offers the risk/reward opportunity for eagle/birdie and safer route for par. By forcing landing zones you can get par 5's that even that the imaginary 300' thrower will have an opportunity to shave a stroke on if played smartly.
I can see how it is confusing though I know a lot of players who'd rather throw the 100'-150' upshot than 3, 300' shots to reach a 900' hole.