looks like Lexan to me. Yes it will scratch. And im guessing it will scratch the tops of your lids as it vibrates and rubs. I think the whole purpose is for the covers to actually take the brunt of the scratches so when you get home from a ride you just pop em off and viola.....pretty lids.
ah nevermind I just saw that they have a "rubber coating" on the inside to cushion it from the bag lid.
Nope. But I don't put plastic covers on my sofa and chairs either. It's a bike.....it's made to be ridden. I'm not saying don't take care of it, in fact I obsess over my bike/paint, but that seems like some serious overkill to me.