I've not had this problem, but I wonder if you could seal (fill up) the pinholes with JB Weld? The gray, high strength stuff has a very long working time and you could spot apply it where you see the holes, pushing it in to fill them. It would not react badly with any part of the trailer and would make a permanent seal. Once cured, you could apply the Kool Seal or another similar elastomeric paint over the whole roof and the repairs would be invisible.
Yes, Eternabond tape would cover and seal the holes too, but it adds some bulk that would probably be visible.
Hi-Lo 1707T - Tire Minder TPMS on Tow Vehicle and Trailer, 300W Solar Battery Charger, Equal-i-zer WDH, Progressive Dynamics Converter, Fan-Tastic Fan
2014 F150 Platinum 4x4 3.5L EcoBoost SCrew