This is strange - it seems the skeleton hands override the normal yellow hands. Just to make sure nothing else was conflicting, I started with unmodded files, and only removed the "customizer_ignore" stuff. Started new save files, found a skeleton in-game, unlocked him. This is what I got in character customization:
The normal yellow hands are now skeleton hands.
I then bought the zombie, having found him earlier - his grey hands were added to the menu, but I still only had two options; yellow hands that were actually skeleton hands, and the zombie's grey hands.
I also bought more characters with yellow hands, but the only yellow hands in the menu still turned into skeleton hands. Go figure.
There are other characters in the game that have slightly different shades of yellow for their hands, perhaps if you have them unlocked you'll have both skeleton hands and normal yellow hands (albeit a slightly wrong shade of yellow) in the menu? I'm gonna check that now.
Edit: Yep!
(Also, notice that white and brown also have two similar but not quite identical shades available to select.)