I tend to think the GPU cooling will be more creative than simply a blower (or worse yet, a bunch of fans) on the GPU itself. The problem, of course, is that anything else breaks compatibility with PC GPUs - but I think Apple probably sees that as an advantage.
It'll either be fan-cooled with a big, slow, quiet fan as part of the computer (not part of the GPU), or it'll be liquid cooled - either way,GPU cooling will be integrated into system cooling. It's possible to build a cooling system that is much quieter per watt dissipated than the standard PC GPU cooling scheme (it would be hard to do worse!). The scheme we have is a hack as GPUs got more and more powerful, but nobody wanted to break compatibility - so manufacturers simply piled on more noisy fans (and power connectors made for other purposes).
Apple will break compatibility and do something better - It'll be powered through the slot and cooled through the system. It may be otherwise standard PCIe (a PCIe slot extended with extra power and the Thunderbolt pass-through connector and with a cooling duct or attached to a cooled plate), it may be a differently-shaped card with an odd connector, or it may be some sort of cartridge design, potentially with mating liquid-cooling connectors. Whatever it is, it will be upgradeable, but it won't be compatible with PC-type PCIe graphics cards. The data interface probably will be PCIe of some sort or another, but it won't be the same power and cooling standards.