I've just spend the last few hours playing Crysis 2 with everything maxxed at 2560x1600 on 2 GTX 680's. One is an EVGA reference card. One is an Asus custom card. Which one do you think was sitting at 77C and which one was sitting at 55C under the same load? I really wish I could put 2 of these asus cards in, but they need space between, and they're 3 slot cards. Without a gap, they get to throttle temp. With a gap, they're amazing.
Maybe that's what the reference cooler has going for it. It doesn't throttle with no gap (it just gets really loud and obnoxious).
I've tried sli with aftermarket cards numerous times and its terrible. I got it working with msi lightning 580s and it was a huge hassle, because while I would get 45-50c at load with single card, 2 of them together made gpu1 go up to 90c in a heartbeat. Yes, my case air flow is perfect and yes there was space in between. Most motherboards require you use specific pci express slots for xfire or SLI, unless you get a quad sli motherboard that costs 350$ (ie, p8z77 premium, Z77 ftw) I know someone who did this with the 580 dc2's and they were fine in single card mode with great temps, but in sli his upper card his 98C at load. Since your lower card dumps heat into the case, it creeps up to gpu1 and turns it into a toaster.
So yes, because of these reasons reference is usually better for sli especially if you're dealing with triple slot cards. They're just a huge pain most of the time. And really, if you're spending that much effort into overclocking why not go water...no matter what on air you will compromise. Reference = good for sli but loud. Aftermarket = limited overclocks most of the time, gpu1 gets too hot. Water = perfect. Just IMO
Anyway, 549.99 MSI lightning with voltage control, and EK water blocks gets me super exited. I loved the msi lightning 580s (despite the initial pain of SLI) they are awesome cards. Twin Frozr is definitely my favorite 2 slot cooler by far, if I were staying air.