I got my Expy back last night. I didn't want to mess with a complete repaint of the roof, so I just had them apply touchup paint to the few trouble spots. The roof line is out of site unless you're standing on the running board. I'm satisfied with the repair and they were nice enough to leave me a fresh bottle of touch up paint. A nice gesture considering I've spent more on gas than what the paint costs taking it to the dealer 3 times for this issue (once for the service writer, once for the body man to give his opinion, and lastly the repair)
I'm certain as our vehicles age, we'll start to see the paint crack off of the roof seal since its a painted elastomer that will flex and the paint will not stick to as well as metal. Mine may be more obvious than others because of my white paint, and the sealant is black. Most vehicles nowadays use a black rubber trim piece to cover the gap.