How tight should I screw my thru-axles?
You should screw your through axle according to the manufacturer's specified torque value range. The torque applied to the axle is not meant to be used for adjusting relative brake/disc position, even if you observe such effect. Keeping the axle under-torqued is dangerous, and over-torquing it might damage the fork/frame dropouts.

A proper solution would be to adjust the position of the brake caliper itself relative to the disc. One possible way to achieve that:


Screw the wheel's axle to manufacturer's recommended torque.
Loosen both bolts that attach the caliper to the fork/frame. Do not unscrew them too much; you should just be able to wobble the caliper by hand.
Squeeze the brake lever so that both pads hug the disc. If the pads were symmetric, then the caliper would become centered relative to the disc. In your case, you should probably do this with a new pair of pads.
Keeping the lever pressed (by using a rubber band, rope etc.), tighten the caliper bolts so that the caliper will stay in the new position. Make sure to tighten these bolts to a proper torque as well (typically in a range 7-9 N×m, but it may be different)


Now, when you release the brake lever, the distance between pads and disc surfaces will be equal (given that both pads move at the same rate, of course).