Were the quarter panel end caps on a Charger painted after installation on the car or were they painted separately and then installed on the car??

Installed on the body, then Painted.

I think all quarter extensions in that era B-body were installed but loose or gapped slightly; reason I say that is the paint didn't bridge the gap, and there was a little overspray on the edges of the mating surfaces. When you see a car that's been repainted with the extensions tight, the paint bridges & fills the gap. Original-paint cars aren't like that.