I can honestly say that I've never heard of the thickness of pads causing ABS issues...

Brakes are really f-ing simple... you have a big cylinder attacked to the pedal then a bunch of hoses that connect that cylinder to a whole bunch of little cylinders which clamp the pads to the discs.

abs is pretty much completely separate, there are sensors in the drive line that monitor wheel speed, that gets fed to a computer module and when it detects that a wheel has "locked up" based on it's speed then it controls a valve in the brake line to pulse the brakes on and off...

I can't possibly imagine a scenario where changing the rotor (or any other part of the brake system) would set off the ABS light. Theoretically you could completely remove all of your calipers and the BMC too and the ABS would be honkey-dorey as long as the sensors and computer module were ok.

thinner pads could make the brakes squishy... but they would have to be REALLY thin... are these R1 concepts rotors thinner than OEM as well? because that would help.

Upgrading to a larger Brake Master Cylinder (or just adjusting the factory BMC if it's possible) would probably solve the squishy brake issue... or just rebuilding the calipers, or upgrading to better fluid... lots of things and improve brake pedal response. In my experience the pads and rotors have little to do with the firmness of the pedal unless they're both REALLY bad to the point where you're exhausting the capacity of the BMC.