Yes, way more pad surface area too. It's a very stout brake setup.
IIRC back in the day there was some independent testing on a GT vs Cobra. On the first stop, the results were about identical. What the Cobra has for advantage with leverage, the GT makes up for with more pad surface area on the front and larger piston clamp force. However, it is on the 2nd and 3rd and so on stops where the rotor mass advantage of the Cobra brakes begins to shine.
So the GT brakes have always been better geared for "drag" type setups, where you want light-weight rotor mass, the ability to fit in 15" wheels, and good stopping power on that first hard brake event. Cobra brakes are more for road-course racing where you are making stop after stop after stop.
With that said, the GT brakes do have one disadvantage that has reared its head after 20 years, in that they tend to stick and seize. For some reason the pistons love to seize in the bore, especially with old water-laden brake fluid and when the car sits. Even remans coming out of the box have this issue. So if you go this route, pay attention to the signs of dragging front brakes.
Oh and to answer your other question, all 94-04 Mustangs use the same rear Varga 38mm calipers. The only difference is the pad support bracket and the pads used, as Cobra/Mach/Bullitt rear rotors are thicker.