Exactly, extra circuitry is required to run two psu's in parrallel, you can't just short them together. And when one psu is connected to the mobo power input(s) and the second psu is plugged into the gpu power input, the two psu's are not shorted together. The power filtration circuitry on the mobo, such as the filter inductors & capacitors is the "extra circuity" even the tiny resistance found in the connections & cabling all contribute to the proper distribution of current, which is why many succesfully run two psu's. Many have also unsuccesfully run psu as there are a million potential stupid mistakes that can be made, and since the method isn't idiot proof, it is considered dangerous Where just using one psu and plugging it into everything is practically idiot proof, and considered the safe, sensible & smart way of doing things.
I may be missing a rather important point here, but aren't multiple rails on a PSU essentially lots of little PSUs connected together? On this PSU, the voltages on the 12v rails at 100% load vary by about .4v but are still all within spec http://www.bit-tech.net/hardware/2007/12/09/enermax_infiniti_650w/3
All the rails on a psu are basically connected together with components such as capacitors and inductors inside the psu case, similar to the types of power filters you'll see on a mobo, but rated at higher currents as they have to power everything, not just the mobo.
I knew this had come up before, but was searching the wrong author. See the ProCooling link from this thread. Adding the current-balancing system as an after-market mod means there's some voltage loss, so the best answer is still to keep the second supply for devices isolated from the motherboard supply. The different voltages (apart from +5VSB) usually come from different taps in the winding on one transformer, each tap followed by a rectifier and LC smoothing. Multiple wires of one voltage usually go to a single pad on the PCB, even when the PSU advertising hype claims "split-rail" or such.
