I think the answer is KISS - Keep It Simple, Stupid.
I think it's just like the $4 fee. It's pretty blunt, and in some situations a bit unfair (for I've always railed that the fee can lead to a family spending more to stay in the back country than in the front country with amenities). But it's pretty darn simple.
Same thing with making all sites to be 'rationed' camp sites. That treats all the campsites equally making the software simpler to implement, and simpler to use.
Besides, based on your own observations, we're talking about campsites that get very little use, and therefore will hardly ever 'fill up' (exceptions being things like a large group that comes thru one of the few sites limited to only 8 campers).
So from a practical stand point, the only thing that is different is that you now have to specify which 'unrationed' campsites you plan to stay at when you make your reservation for a 'rationed' campsite.