Why are the 11.75 Brake Better?

There are options. You can (or used to) get Hawk racing pads.
I searched Hawk's website and can't find anything for classic Mopars. I know EBC sells pads for them though. Dr. Diff includes pads in their kit I might send an email and ask what brand/type they are.

Another note, the piston area of the 2-piston Cobra calipers is almost half of the 2.75" single-piston Mopar calipers. Doesn't that mean the clamping force is also much lower? I guess the bigger 13" rotors make up that difference? Oh yeah... and a ton lighter too lol I forgot about that part.

Looking on AmericanMuscle.com there are bolt-on brake upgrade kits for SN95 Mustangs from Baer, Brembo, Wilwood etc. so if you have the caliper brackets and rotor adapter hubs for our classic Mopars there's room to grow if you want to have a real race-ready track machine.