I know msi has excellent cooling.
My gpu idles at 24 and has never gone over 60 at load with most heaviest game out there and after hours of play, not to mention it's very quiet.
Keep in mind msi is more then likely going to use a custom pcb not just 'evga' overclock you can do yourself and call it o.c edition.
580's have a lot more power so I would imagine they would run hotter especially in sli.
Top card gains about 10 degrees if I am not wrong but if you're going after market solution then it's all good.
At the end of the day, it's whatever your personal preference is and what YOU think is best. If i was in your position I know what I would personally go for.
Good luck either way.
I'm not worried about the top card due to the fact my board i can populate in PCI-E 1 and PCI-E 5 slots to give the top card more space, typically yielding only a 5C temp increase in the case of my 560s and seemingly same temperatures with my temp 9800GX2 configuration.