What if yellow sunlight changes the quantum phase of a kryptonian body or kryptonian matter, to mimic the wave function phase of so called "neutronium" or other potentially indestructable materials, thereby making flesh and bone as tough as indestructible matter, but without the weight or other characteristics? This durablility would also allow for ultra strenght and speed potentials (I say potential because they'd be useless without the juice to run them) due to the correlation between muscle strength and speed being higher with durability.
Another thing about durability is that the protein structures that make up kryptonian bone and muscle could be based on carbon nano tubes, which are pound for pound 600 times stronger than steel.
Cool thoughts re: quantum phases. I suppose you're suggesting something like in-phase virtual particle fields in the EM, grav, etc. virtual fields surrounding all matter here. Given that infinite virtual particle density, making them act in phase would render them pretty much indestructible to anything phased like that.
Another angle that could augment the above is negative mass/positive mass interactions in those same fields. Negative mass repels positive mass but due to its negative inertial properties is still attracted to the positive mass. The net result is the neg object scoots away while the pos one chases after it in a smoothly accelerating manner. Properly constructed and balanced, a pos/neg mass construct would be truly immovable since a force acting on one aspect would be countered by the reaction of the other aspect.
As for the carbon nanotubes, that is a good idea and probably one implemented by the bioengineers back home on Krypton or Daxam. Be aware that contrary to popular notions, the covalent bonds in biomatter are actually the strongest ones in nature, not the metallic ones commonly used in our machines. If the covalent bonds in butter were properly aligned and utilized, it would be several orders of magnitude stronger than the steel knife used to cut it. Similarly, rubber if so coherently aligned would be stronger than steel (think of a rubber band that actually tended to get stronger as it was stretched instead of the individual molecular fibres getting broken one at a time). IOW, even without invoking nanotubes, better organization of existing molecular structures would give some pretty impressive material strengths.
BTW, that was one of my objections to Wolverton's book The Science of Superman. He supposed heavy metal deposition to augment Kryptonian flesh when metals are actually weaker than the existing bonds so better organization of bonds makes more sense and requires no extra 'metallic absorption/deposition' concept which makes Wolverton's idea a bit ad hoc.