depends on a few things, is the game a classic? (some games are more blasphemy to mod than others). also its cond is important- it is really hard to ruin something that is all ready ruined.
i try to go conservative, but in the back of my head i know any time i break out any paint or what not i am truly ruining orignality of that machine! no matter how good of a job i do. i live with stuff i dont really like just to keep machines org at times.
also sometimes i would only mod a machine i plan on keeping for a long time- you will seldom get labor time back, and i think its best to let later owners have the ability take something the direction they want to go with out undoing your attempts.....
that said it your machine, that sits in your house, nothing wrong with makeing to pleasing to your eye.
you can sometime mod something with limited trouble to get it back to org cond.