The flexing of the forks/axle/caliper mounts as well as any run-out present in the rotors themselves causes the pads to retract. This action occurs immediately while riding so we have much more clearance of pad to rotor.
Not the case as we pull up to a stop, and take our measurements. The only pad retraction influence is from the hysteresis or springiness of the piston seals which is very minor.
If you want to measure pad drag, buy a cheap infrared temperature gun and check rotor temps at various times. Alternatively, stop your bike without using your front (or back if linked) brake, then lift and spin the wheel.
Any residue left on the rotors from the application of cleaning agents will affect the friction performance of your brakes. If you feel you need to clean them, soapy water with a good rinse is fine. Or, for deep cleaning to remove old pad deposits use a high grade acetone as that will leave the least residue.
Hand sanding a rotor is pointless, you will never remove any old pad residue that way. The only way to efficiently smooth/clean a rotor is with a specialized rotor hone or flat hone.
If your rotors are turning blue from heat, then yes, you should be concerned, but I suspect that condition is very rare for the folks posting on this board.
Take it or leave it, it's free advice.

Fretka