Decent racks these days all have some sort of anti-sway system built into the arms or frame cradles. So bikes stay separated and don't swing. Then it's usually a question of making sure the pedals aren't going to turn and get to where they can hit anything. A bungee takes care of that. I try to never tie or trap the wheels so they can't spin, because I've seen too many examples of tires burnt from exhaust heat. The spinning prevents that more effectively than anything else.

Eons ago when we'd just pile bikes onto racks with simple arms and no cradles I used to go the the carpet company and ask for the samples of discontinued carpets. They'd give me a few for free, and I'd punch holes and load them onto the racks between the bikes, but that era is long past.

OTOH- I'm very blase about my bikes which I routinely toss into a car with wheels off and placed on top. IMO bikes for riding and enjoying, not obsessing about. I've tossed my best bikes into bus bellies and pick up beds, onto trains, ferries, and airplanes (before box rules) --- I was once paged at JFK airport to come and untangle 12 bikes I'd loaded into an Electra, which had settled into a tangled mess during the flight. Also tied them to the pontoons of a seaplane, and the rails of sailboats.

If you start worrying about your bike, it'll limit your options. While some obsess about every ding an nick, I consider them souvenirs of the good times we've had together.