I have somewhat of the same question - but remain puzzled... I unlocked the Flyer's bootloader yesterday through HTCdev, flashed a Revolutionary recovery (based on CWM) through fastboot and could then install SuperUser through an update.zip in the stock ROM.
I have mode some development on other devices, so I'm familiar with bootloaders and stuff. The forums are mostly talking about S-OFF and I don't really understand how that concerns me, because now that my stock ROM is rooted, I can do whatever I like (remove bloat etc.). I may not understand all implications of S-ON, but I know that my bootloader tells me my Flyer is S-ON.
Now, is there any problem to flash another ROM through CW Recovery? Will, for example, LeeDroid's ROM replace anything connected to 3G (I have the model running on AWS frequencies, which are quite unusual). Could I simply flash LeeDroid's ROM, then get back to my stock backup without any problem?
I guess the question is; since my bootloader is unlocked, does S-ON or OFF concern me in any way? Or is S-OFF only important for those who can't unlock their bootloaders through HTCdev?
(I do promise to write something up for the wiki if ever I understand :)