Sounds like someone just doesn't feel like modding such a tedious undertaking themselves...!
But seriously, it would be kinda cool to reward players that run an entire fleet of a single faction ship type (pirate, TT, LP, XIV, etc.) with what is basically reputation free piracy, where the faction that your ships look like gets blamed instead (ie, a false flag incident); if you fail/lose/get "caught," you lose rep with both factions. However, adding a paint recoloring action would basically negate the point of the previous suggestion. So basically, no, a paint shop is bad idea, lots of mechanical turk work with little payoff beyond aesthetics. I would rather have Alex play with fluid dynamics code so that battles which occur in solar flare or neutron star beam look way way waaay cooler. Or at least more system backgrounds like the Unknown Skies mod, or the low-orbit battle maps in the Scy Nation mod.