In our case, the main reason is that the top of the rear rack isn't available. This is where we carry our flight bags or food items.

1. for a relatively short open-jaw tour (i.e fly into city A and return from city B), we ride out/in the airport and use padded flight bags. We prefer padded flight bags over the thin plastic bag used by most airlines and would rather not spend a day hunting for a box at the nearest bike shop and deal with the logistics of finding ground transportation for two boxed bikes. (Bags are also mandatory on several trains).

2. we find it simpler to store the same stuff in panniers and to deal with transient goods (mostly food) with rack tops. Our routine was to use one (green) pannier to carry mats, sleeping bags, chairs and tent for two. It all fits well in a 20L roller.

This being said, as our next trip is a loop, we will consider the possibility of storing our flight bags near the airport. This would free the rear rack's top.