Carbon is almost always painted with at least a clear coat, mostly for UV protection I think. The clear coat cracking/chipping can give you a heads up about cracks or damage, causes many false alarms as well though.

Check silly things like QR skewers tight? Specifically with some Trek bikes I've seen a loose derailleur hanger combined with a loose skewer cause all sorts of weird noise.

Don't be afraid to take it to a Trek dealer or at least email some pictures to Trek. Visible damage or not assuming everything is tight and shouldn't be causing noise it's worth checking out.