I've been buisy so didn't have time to see if anyone answered, but here's my spin on things:
The impure resurrection does not require the full corpse to ressurrect, right? Only enough DNA is needed to "resurrect" the dead. It's not a re-animation or puppet technique per-say (there are no chakra strings). The "resurrection" process is different from the Christian based belief that Jesus Christ our Lord and Savior raised from the dead and his corpse wasn't found. Basically, christ's spirit left his body when he died on the cross. Shit happened, and he re-entered his body on the third day.
With the impure ressurection jutsu, since only DNA is needed (not the full body) the nagato that is moving around could have been "grown" from a skin cell, blood sample, or his foot. The process could be like organ growing from stem cells. Essentially, the ppl we see moving around are not necessarily in their original bodies. Thus, from growing nagato and itachi from cells, the DNA would dictate the growth of their eyes. DNA is lint the master recipe specific to the "owner". If mandara died and was re-animated, he could have both eyes, even though 1 "died". That's where speculation comes in...
But, we can deduce that the physical forms are not the original. If so, the 1st and 2nd hokages (when orochimaru attacked 3rd) would have been all moldy and decayed... Eeeewwwwwwww.....
So, nagato's corse can still be wrapped in paper, eyeless. (tobi/mandara has at least 1 "on"). There are 2 physical forms of nagato, hypothetically. The jutsu uses the DNA sample the harness the soul and chakra of the person. Even if you loose an eye, arm, toe, finger,.... Your DNA still says that you have one. That's why stemcell research is sooooo big. Stem cells have yet to specialize and can be used to grow into needed cells like brain tissue. The DNA us the master plan.
Also, when the ppl "move on" they crumble and turn to dust. Obviously not the original body.
DNA mutations would hypathetically carry over. So, danzo would be resurrected with 1st hokage arm and tree jutsu. Sharingan arm??? Idk, if affected DNA, then yes. But this is a manga, fiction = fiction. Applying logic and science of real world cannot always lead to consistent results.