Man you are lucky they used those screws. They are actually incredible strong screws, even rusted. i saved many of them and they are the choice screw i reuse elsewhere where strength is required.
My starcraft conversion roof used standard drywall screws which rust instantly when breathed upon, and these started the roof gutter rust battle and the war I am destined to lose.
The screws along the leading edge of the roof are trying to pierce sheet metal at a super tangential angle, and often they grab nothing, and do nothing but scratch the paint down to bare steel. Of the 14 or some such number of screws holding my roof down, only 4 actually made it into steel and achieved anything.
As far as what was originally used between aluminum and fiberglass, I do not know.
I did not care about appearance and discarded the aluminum strip and trim piece and used self drilling #8 stainless steel sheet metal screws with captive washer and O ring. All the hexagonal bolt heads are quite visible around roof perimeter, every 4 inches.
What I would use in your situation, is some type of weather stripping product listed on this page:
http://www.mcmaster.com/#standard-rubber-weatherstripping-strips/=128d0e0Look for good UV resistance.
I'd recommend against silicone caulk to fill the gaps, It will eventually fail, and leak, and nothing sticks to silicone, not even more silicone, so complete mechanical removal and then a solvent to clean the paint will be required to reapply more of it which will also eventually fail. Lather rinse repeat, shake fist at sky, throw tools, ect