Although I wouldn’t normally consider doing such an extensive cosmetic-only modification during this EA stage (other considerations take priority), this certainly seems to be a popular idea. Some unorganized thoughts:
Paintjobs in CIU are 25% the size of CI5’s.
How would these rekins be applied? You mention per spaceship, but how exactly? If it’s a variation of a weapon equipment (like rarity), you’ll only be able to change a single weapon per mission. Hardpoints? Mission slots?
Are these skins equally valuable/rare? Off the top of my head, the most efficient way to implement this would be to piggy-back them onto rarities (so you get a e.g. common/uncommon/rare/legendary neutron gun), but that would mean (a) some rekins are rarer (hence more valuable?) than others and (b) what I said before, you’d only be able to activate a single one at a time.
Gift colors would probably need to stay the same (the combinatorial logistics of trying to re-color them while also making them sufficiently discrete in all cases would be a nightmare).