>I thought the zones being unknowable was part of the story.
I'm prepared to call unknowability unscientific.
>a cheap way of avoiding singularity issues muddling up the plot.
Yeah, exactly. They weren't an interesting idea so much as a cheap hack.
The Magellanic Cloud aliens created (or at least can manipulate) the zones to stop transcendental "things" like The Blight from destroying all sentience (and then becoming a problem for the Cloudies?).
The zones are two things: a few layers of "play nice, you guys" and a cheap way of avoiding singularity issues muddling up the plot.