Indeed it is even a stiffer rubber or plastic than an actual tire.
I'm, too, afraid of messing it up some product besides water. When I clean my figures every year I use a humid cloth over the tires to remove dust and give it a bit of moisture (once or twice a year may not be enough, though)
Kaneda's clothes have faded and the red is kind of dusting of in some parts (like the shoulders where the jacket is folded over itself). The back decal has pealed (maybe because it is in contact with the rubber seat). Everything else looks fine.
I love this set. Wish I could maintain it for as long as it would be possible... Of course, nothing is forever and we should not stress about it.
For now the solution would be finding a customizer to make an even better job than Medicom.
maybe once it fully flakes someone can finally try the rubber dip coating method to see if it works.