Its hard to make recommendations about repairs when not familiar with your specific boat and how your wet exhaust is constructed and no pictures... (not picking on you, just sayin), BUT;
Yes, epoxy will stick to PVC. When gluing PVC material to the transom of an inflatable boat, WEST system G-10 epoxy is recommended. This is a good product because it is pre-thickened, and if you don't need a large amount you are not having to buy it by the quart or gallon.
With that said, I hope you are not planning to use PVC plumbing grade pipe in the place of fiberglass tube? Not a good idea in a wet exhaust application. Your exhaust tubing should be marine rated wet exhaust hose like SHIELDS series 250 or Trident in rubber or silicone.
I am assuming the fiberglass tubing you are talking about is only what enters and exits the box, cut a short length to make a flange where the appropriate wet exhaust tube will be clamped? A good source for fiberglass tube in short lengths at a competitive price is Goodwinds.com
Epoxy is better than Polyester resin, hands down. Temp should not be an issue, the point of a wet exhaust is to reduce temps in the exhaust system. Polyester resin does not have a very good secondary bond strength when repairs are done on previously cured polyester resin. You would be correct in doing your repairs with epoxy.
I hope this helps... without pictures of the system and the damage that needs repair it is just my best guess based on the info provided.