ive only seen that happen once and that was on a tundra that had 2 inch or so spring spacers and it was suspected that the shock bottomed out hard, but even then it was the shock body that was destroyed and not so much the strut rod. maybe the rod had a small fracture and it finally let loose but i dont think that the rotate and alignment had anything to do with it, unless they decided to beat on the shock during the service for no reason.
as for the axle i would just do a reboot unless theres some seroius damage to the axle shaft or joint bell that cant bee seen on the pics. nothing special about removing the axle, i would usually use two pry bars between the inner joint bell and the axle housing to pop it out, or use a hammer and prybar to hit it out. if it dosnt want to come out sometimes rotating the axle a little bit will help with getting the c-clip on the axle into the right spot and it will come out easier
as for the axle i would just do a reboot unless theres some seroius damage to the axle shaft or joint bell that cant bee seen on the pics. nothing special about removing the axle, i would usually use two pry bars between the inner joint bell and the axle housing to pop it out, or use a hammer and prybar to hit it out. if it dosnt want to come out sometimes rotating the axle a little bit will help with getting the c-clip on the axle into the right spot and it will come out easier