Although I'm not 100% how a fan does it's management of the motor I'd assume it energizes 2, 4 or 8 electromagnets that pull the fan hub.
So in essence I think instead of the controller going: 1-2-3-4-1-2-3-4 it goes 4-3-2-1-4-3-2-1. This might be overly simplified, but wouldn't that be the easiest way to do it?
Well...the average fan's onboard controller is not a particularly smart piece of circuitry, just transistors, resistors and a Hall sensor IC:
http://pcbheaven.com/wikipages/How_PC_Fans_Work/
But notice what's in the diagram for the 3-wire fan? It's only got 2 transistors and you need 4 to run a fan both ways (making the H in H-bridge).
You are correct in that if there is enough PCB space for some extra components, a fan is perfectly capable of doing such a thing and I suspect that is MSI and Enermax's approach.
However, this places a limitation on control unless the fan is PWM and both the fan and the Super IO are in agreement on what constitutes forward and backwards.
So actually, I need to make a addendum to my original statement...
Well, H-Bridges are not terribly space efficient (the few ICs I've found that will do 12W are the size of old school DIP packages) and with the proliferation of Mini-ITX and smaller boards, it doesn't seem like a good value proposition. You could fit in another RGB LED driver or 3 in that space. Also I'm not sure if your average Super IO chip can change PWM frequencies.
For this approach to work, the fan itself needs to be 100% "dumb", just 2 wires directly attached to the motor. You can farm the H-bridge onto the fan itself probably with a control element but my point about the Super IO's limitations still stand.
Boy, did we get off topic. Apologies.