Wasn't Safari/WebKit largely based on KHTML in the beginning? This doesn't say it wasn't, but seems to imply that there was a separation of the two that was more complete than it really was.
I realize the OP is in a better position than I to know exactly what the reasoning here was, but it seems like reporting yourself as KHTML when you are largely based on the KHTML rendering engine would just be a sensible and practical thing to do outside of all this cloak and dagger stuff.
(Granted, I doubt there were very many websites, if any at all, that gave a rat's ass about special cases for KHTML compatibility).