Thanks, ATDrake, for the helpful hints and new and updated links.
So I guess I can't tell the difference between kindlegen for the PC not generating waypoints, and K4PC not showing them, but after changing Cordelia's Honor's content.opf file to have only "en-us" in the <dc:language> tag (got an error the first time), then it generated successfully, and shows no waypoints on K4PC.
Will send that to my friend with a hardware kindle and see if it has waypoints there.
Hmm. OK, Kindle Previewer shows the waypoints like you suggested. However, it seems Kindle Previewer is named Kindle Previewer rather than Kindle Emulator for a reason... I can't figure out any way to do a search in Kindle Previewer.
However, my waypoints show up fine, and I can hop between chapters, so that is good! I'm at only 10% of the limits of the guy that ran into the limits of 4064 waypoints, so I'll let him push the limits.
I note that even after seeing waypoints on Kindle Previewer, I still find nothing like them in K4PC, so I guess it is just a missing feature. K4PC does have search, though, of some sort.
But that sort of lessens the benefit of Kindle as a cross-platform viewer tool, if each of the tools has a different subset of Kindle features. I can understand that on different platforms, some features may have to be implemented differently, due to different hardware controls/controllers, but it seems that the features should all be there
Oh well, maybe someday. Another friend tells me that search isn't implemented in K4Blackberry... I'll have to ask him about waypoints... but if K4PC doesn't do them, it seems unlikely that a search-free K4BB will.