In principle, I agree that sometimes sacrificing rigor for clarity is justified. But in the case of the Theory of Patches, not a lot of people have managed to understand it in detail. (I say this based on about a year of lurking on the darcs-users mailing list, some time ago.) If in addition to being opaque it's also not rigorous, that's a bit of a shame.

That takes nothing away from darcs as a piece of software, though. You don't have to understand the theory in order to use the tool, and it really introduces a revolutionary way of thinking about version control.