However, if you read carefully, and consider some of the consequences, it becomes clear that this is not a natural rule of the universe, but something technological, created by presumably one of the first civilizations to become highly technological as a defense against what would otherwise be a fairly vicious universe with constant high-tech civilizations fighting each other with frightfully powerful weapons, and perhaps a hint of compassion towards the not-yet-high-tech civilizations. That's why it can be manipulated with certain keys, in ways that would not be possible (lots of FTL signalling) if the Zones were truly a fundamental rule of the universe. (Notice also how the super-high-tech civilizations don't understand how the Zones work or why they exist, which if there were purely natural seems unlikely.) The Powers tend to last 10 years probably because that's how long it takes to either be accepted by the highly advanced civilization(s) that live in the galactic cores, or how long it takes to work out how to move there despite the Zones being in the way, or both. This creates an entrance gate against things like the main threat of the novel getting into your high-tech civ.
I don't deny I'm extrapolating a bit, but there's a lot of hints, especially if you add A Deepness in the Sky to the mix. Pham was probably sent from this central civ to fight A Fire Upon the Deep's main threat, if you read where he came from. The entire planet of A Deepness in the Sky is clearly from a super-high tech civ far beyond what Earth's depth could support, but it's from closer to the galaxy's core, not farther, which is why Pham went in to the galaxy's core after that story rather than out looking for more intelligent life. He in fact found it, or it found him, if you prefer.
Once you see there's a probably-even-beyond-Transcend civilization living under the Zones of Thought it mostly comes together.