Flying with a packed Swift, I've experienced both problems you mention.

chipped paint: Visit a 99¢ store or something similar and shop for cheap towels. I bought black hand towels at 3 for $2. Hey! They're starting out black; it won't get much worse. Use the towels to wrap the bike parts that are getting smacked by other hard stuff; works for me.

security inspections: Security Net used to protect your bike if TSA opens the case I haven't bought / used these nets, but a friend who regularly flies with a Bilenky Bilenky Cycle Works tells me that most of the time, the S & S nets work as intended.