Livre d'Or

No vehement defense here. I'm less convinced than you that there's 200 pages worth saving in there. I didn't find it smug, though I did find it a bit much self-satisfied with its cleverness, but I was willing to give it a pass on that for playfulness.

I do disagree with you on one matters of fact and think another you may have missed. Re the first, Stephenson is very much not saying "wouldn't it be great if geeks ran the world". The apert system he both sets up and interrogates, which, as someone who knows a modest amount about the history of monasticism in the West, I find really intriguing. He makes an argument than any ivory tower can basically be a Roach Motel(tm) for intellectual troublemakers. By removing the geeks from society, that system renders them pure but almost entirely impotent in it. Then later in the book when the geeks break loose, they do get their moment of heroism, but in no way which suggests they'd be great at running things.

Re the second, the similar-but-different language is, itself, part of the whole downstream-Platonic-parallel-world thing, and as such is essentially foreshadowing. That is, there are cognates in this world for their words because this world is a pale shadow of theirs. Those invented words aren't just to make strange another world, they're illustrating the relationship of that world to this -- just very slightly off.