Not really sure here, but if I remember well S-On/Off relates to security primarily, whilst the unlocking process relates more to the bootloading, allowing you to change booting sequence for instance. Not sure whether by unlocking you are simply telling the phone to disregard the S-ON/OFF status. Someone else can maybe explain better? In my case, I unlocked, S-OFFed and rooted three devices so far, two Wildfires and a ChaCha. In each case, I kept going with S-OFF and root cuz instructions said so. Once you unlock, I think it's best to proceed that way if there are instructions. I still think that in the dev community though flashing custom ROMS/recoveries straight after an unlock process is still not popular / frequently visited in forums.