Hmm...Many touch up methods.
Base clear IS touchupable...Your body guy is kinda like...meh
Being a repaint, Id be a little incined to say thir color isn't exactly 100% true to factory, and it might be better to have them make you a 4 oz bottle of touch up paint.
From here there's quite a few things you can do.easy way in your case... You could apply the paint to the scratch, unreduced. let the paint fill the scratch, but keep it in the lines.Keep it nice and tidy. Let it dry, and then go over it with........Clear nail polish
Once again, keep the paint / polsih within the boundries of the scratch. If you have some good quality rubbing compund, you can hand buff the area to further make the scratch disapear. If you're really anal, before you buff it, you can wetsand the area of the scratch with 1500-200 grit sand paper