As an old fan of Silver Age Superman, my head canon is that when Supes set himself and absorbed force from bullets, he was, perhaps subconsciously, using his power of flight† to resist the concussions. His insides were as invulnerable as his skin. Next you will be telling us Kal can't push a planet with his bare hands, nor tow a string of them with an inertron chain!

† I ascribe to the idea that, in addition to making leaps with super-powerful legs in low Terran gravity, Superman has a super-charged ability to emit anti-gravitons. Kryptonians evolved this ability (or were genetically engineered to have it) in order to be even able to stand in Krypton-normal gravity.