This reminds me deeply of Borges: https://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevole...
To me, that bit of Borges is a reminder that all human taxonomies are limited and provisional. But it seems to me that Cyc and its brethren are built around the notion that a universal taxonomy is important and achievable. I guess it's possible that a useful kind of cognition could happen that way, but it's patently not how people work. If I had gotten to the point where I was forced to define exactly when a tree got a soul, I hope I'd realize that I was barking up the wrong tree.
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.