I'm no expert on the subject, but my view on why bigger brakes are better while using the same ABS unit is as follows: When you are using the same master cylinder with the same ABS unitl, there will be essentially the same amount of hydraulic pressure applied to the brake system. By simple math, you know that by increasing the piston surface area you will increase the net clamping force that can be applied to the pads and rotors. Increasing the effective surface area of the pad has the same effect, so there is no sense in going to a caliper with more pistons and smaller pads area since thats kind of counter-productive. Now, by going to a larger rotor, this clampin force is being applied at a farther distance from the hub center, and is capable of producing more braking "torque", so to speak, than a smaller rotor using the same caliper/pad surface area. This increase in leverage obviously increases your stopping power.
Now, this is all common-sense stuff. But the area that I can understand you're having trouble with is if there is more clamping force/leverage with Cobra brakes, won't the wheels lock-up easier? Well, in theory, yes. But what is happening is that the the ABS unit will pulsate the hydraulic pressure at the same frequency as with the stock system, the difference being that the Cobra brakes will provide greater clamping force and brake leverage between each pulsation, resulting in a greater reduction in rotor speed between each pulsation, without locking-up the wheel. Now you might also ask, won't the larger brakes tend to fade more because the instantaneous velocity of the area of the rotor contacting the pad is greater than on a stock smaller diameter rotor, and will therefore create more heat? Well this is true, but that all lies in the pad and rotor design, and their ability to dissipate heat and gases.
So the short answer from my point of view is, bigger is better when it comes to an ABS-equipped car