I'd imagine that you are overclocking both cards via software if you are running SLI. It might not be stated explicitly in the program, but that would be the only thing that made sense to me. You can use NTune to overclock your card as well and it may show you the information you want to see (each individual card).
Anyway, I prefer flashing the bios too but I wouldn't really recommend it for novice users. And its not all that dangerous; despite me changing random bytes in the rom and still flashing it to the card, I still had a perfectly functional card. In fact, I've never been able to break a card although I stopped trying (not bored anymore). As long as you use the rom dumped from your own card, then its pretty hard to cause permanent damage.
Always works as long as NvFlash supports your card (you don't NEED NiBiTor but even advanced users might be jittery not using it)
Operating System Independent (provided nvidia makes drivers for your OS)
No dependence on software
Permanently remove Dell/Nvidia underclock
"Unlock" card (with one of two roms :/ )
May be your only option
Reduce EEPROM life cycle (but EEPROM is rated for 100,000+ uses)
Steeper learning curve
Short answer is, that although it may be unnecessary here, flashing provides many benefits that you cannot get in software.
Without these boot cd's on the net, I doubt we'd have any "bad flashes". We'd have far less users overclocking but meh, I guess they'd learn the stuff if they wanted to overclock.