I've heard not to use silicone based products, but how about 100% carnauba waxes?
I got to borrow an Ibanez S from my cousin yesterday and am in the process of cleaning her up ang getting ready to string. But, I can't help thinking even after I used Dunlop formula 51 on her, she still looks a bit dull on the paint. Can you theoretically apply cleaner wax/scratch removal products, wax, claybars, etc to them? Wood, primer, paint, clear, it seems as if they're pretty much the same. Correct me if I'm wrong though..
I, too, have used automotive wax on my guitar projects but not any kind of polishing compounds. A factory finished guitar should have a few coats of clear on it so I would first try to fill in light scratches with wax before rubbing out with a polish.
I've also used Mother's metal polish on chromed bridge parts to take down light surface rust, corrosion, and crud but go light as guitar bits have thin chroming layers.
If the finish is painted and cleared yes you can. I have used both Mothers Wax and Liquid Glass Polish on my Strat, Parker, Ovation, and J-Bass. Everything else I own is either a matte finish, wood, or poly-coated. I have also used Mothers Metal Polish on Nickel hardware which does fine as well.