Tom, I've used both bags and boxes for transporting my Raven by air. Never had any problems with the hub with either covering (nor any other problem, fingers crossed.)
I always put big arrows to signify "this side up", but I have no idea whether the bike was stowed on its side, or vertically.
Best wishes to you and Kathy for safe transport of the bikes, and safe journeys over the ground!
Cheers, John