Seams would be sealed and sound deadener applied to the inner surface of the rear quarter panels at the start.
You would have the trunk lid attached (so all the mounting bolts and hinges in place) quarter extensions in place (though spaced outward using something other than the final nuts) And (if so equipped) the rear bumper brackets in place so the bolt heads exposed in the trunk would be there also.
Over all of this the exterior color would be applied. No great effort (so little or to some overspray depending on surrounding panels) was made to cover the bottoms of the rear package tray and or the quarter panels. A nice finish coat was applied to all visible surfaces, and its not uncommon IMHO to find a run on the bottom of the trunk lid or on one of the wheel tubs - just happened
Guessing that you have a 65 or 66 fastback so here are a few examples
Note that the blue fastback apparently had its trap door hinges replaced at some point as well as a little paint touch up on the drivers side. You can see the overspray on the back side of the interior trim panels that should be an off white on the trunk side
Hope these help