Originally Posted by cpach

It would be helpful if you mentioned the exact make and model of the brake. You mentioned that the clearance to the pad that was not rubbing seemed very close. This may or may not be wrong--pads on disc brakes are spaced very close because the system can operate with higher mechanical advantage with the pads closer, particularly if the pads travel at a linear rate as the lever is pulled, which varies by brand/model.

However, not infrequently on new bikes, particularly on brakes that are actuated by DOT fluid there will be too much fluid in the system which will space the pads too close to the rotor.

If your bike was in my stand, I'd first center the caliper so that the disc was centered between the pads Loosening the brake mounting bolts, squeezing the lever, and tightening them down SHOULD center the caliper correctly, but often due to some kind of friction this doesn't work, and I always double check and frequently have to slightly loosen the bolts to align them by hand. Be careful to never do this with the wheel moving--I ended up in the ER with a bisected fingernail trying to adjust a caliper with the wheel moving this year.

Then, if I determined that the pads were too close to the rotor, I'd remove the pads and open up the lever bleed port, cover it with a rag, and them press the pistons out to force out any excessive fluid, then close the bleed port, clean up the lever, and reinstall the pads, and recheck. I've built a handful of new bikes that needed this with SRAM brakes.

Also, the cases of pads wearing out involve racing in extremely muddy conditions, and were mostly problematic with cable-actuated disc brakes (because they don't automatically advance the pads as they wear). It would be extraordinary if you did excessive wear with the riding you've described. My advice for your cross bike is to ride it wherever you feel you want to. My experience is that the relative lack of traction and the brutalness of riding a rigid bike with not-particularly-wide tires results in a pretty cautious approach to riding semi-technical singletrack, and I've felt pretty safe about the bike, even when not feeling safe about myself.