I have the same problem with trunk bags, even on a standard rack, not enough clearance with the seat. I did what you did in the second picture, turned the bag around. Plus, the other way it would touch my rear end and drive me nuts. The only thing that was a problem was I no longer could hang a light off the bag. I got a mount so I could attach it to my rack.
Trek Madone 4.7 WSD
Cannondale Quick4
1969 Schwinn Collegiate, original owner
Terry Classic
Richard Feynman: “The first principle is that you must not fool yourself and you are the easiest person to fool.”