The lesson I take from the fact that universal ontologies are untenable is that human cognition isn't driven by ontology, so the quest to make a thinking thing out of pile of symbolic logic is one that has no guarantee of succeeding. I think Cyc's whole project is roughly similar to the Frankensteinian notion that if you just put together the right parts and provide a vital spark, you'll get a living being. It might work and it might not, but either way it's not science; it's sympathetic magic with the trapping of science.
And yes Cyc ontology wasn't consistent. Lenat's point was that it is impossible to have an ontology consistent. Which makes sense given how there is no consistence across human society or even every individual human.
I also don't think it was Lenat's original point to have an inconsistent ontology, as evidenced by his early projects. I agree that he eventually had to admit that. What I'm saying is that when he admitted that he should have recognized that it cut at the heart of what he was up to. Something I think borne out by the fact that he spent his whole life on something that didn't succeed on its own terms.