The obvious answer is that there are different heatsinks and fans for cooling on the non-reference cards. Sometimes non-reference cards will have upgraded components and an enhanced power design. Finally, some non-reference cards will come with higher binned GPU chips that have passed a higher level of quality control. Usually higher binned chips are selected to guarantee more consistent performance when overclocked.
Without more specific information about the Sapphire card you are considering, I can't advise any better than just generalizations.
Yes. The differences generally come in the form of higher stock clocks (though that's not important, as you can just raise the clocks yourself), better cooling through different fans and heatsinks and, occasionally, better fan profiles than reference designs.
Sapphire's cards generally have two fans, so they run cooler and quieter than reference cards but vent all their heat into the case instead of ejecting it out the back. This is fine if you have decent case ventilation, but if you don't your card can end up hotter than an external-exhaust reference design would.