"Polycarbonate" is
plastic. "Fiberglass" is slang as far as I'm concerned...they are Fiberglass-Reinforced-
Plastic(FRP). There is good and bad quality panels in either of these catagories and even plain old unreinforced resin panels...which you guessed it, are also
PLASTIC. Could be polyesters, vinylesters, PVCs, etc...or blends. Some thermoset, some thermoplastic.
You need to dig a bit deeper. FRP in general is more stable (shrinks/grows less) in hot or cold temperatures. This may or may not be important.
UV resistence (to brevent them getting brittle after sun exposure) can be done with additives, certain resins or a coating applied to one side of the panel. For polycarbonate panels, it's usually done with a coating so you need to get them right side up when installing. Very sunny areas need to pay extra attention to how the panel resists UV.
Pink insulation is fiberglass...but not pure. Boats are not fiberglass, they would sink...they are fiberglass-reinforced whatever resin. Corvette body panels are fiberglass reinforced plastic (polyesters mostly along with a healthy dose of limestone filler), not "fiberglass bodies". Fiberglass isn't even the highest percentage ingredient. Same with fishing poles, skis, etc., etc.
And don't get me started on "carbon fiber".
I doubt your over heating is because of the sky lights.
If you climb up and touch them you will probably find the metal sheets hotter than the plastic.
You need some venting.
Seriously????????? You've never felt the heat standing next to a window exposed to the sun. Never seen a dog or cat curl up near a window on a sunny winter day. The fact that the metal heats up more does not mean it is transmitting more heat. But yeah...regardless, venting would likely help if done correctly.