I have found that the rear pads on mine will wear down, but the brake fluid level sensor sometimes doesnt pick up the lower level of fluid unless you unscrew the brake fluid cap and tighten it back ( air lock i suppose?). So the rear ones on my mk5 gti should have a warning light via the brake fluid sensor but not always the case.
Yes i think calipers dont like to have the piston come all the way out, and some have issues thereafter from my experience. Maybe if the piston rubber is crap and if the piston is all the way out, then its more likely to get dirt or corrosion on the piston which can cause it to seize. The front near side on my gti 2006 has a brake pad sensor within the pad that brakes a circuit contact and throws up a warning light to let you know when to change the front. I suppose its down to you really and if your brake pads are expensive, like EBC and how heavy you are with braking. The difference between 3mm and like 5mm would probably be heat and more fluid requirements? maybe? 3mm isnt something id personally run with just because it doesnt give me much time to replace, and if your heavy braking with the piston all the way out iso to speak, id think its hydraulic nature would be at its limit. So i guess it depends? age of car, fluid level, heavy or light braking, cost of brake pads, time you have left to change them etc
One thing i have noticed on my vw, if the brake pad sliders are not free of crap, especially on the rear, the parts that slide against the brake mount, then one brake pad will take more pressure than the other. Common knowledge but something to definetly look out for when you change or inspect your pads i suppose
