...a flight from A to B, which are in the same zone, but the only way to get from one to another is via a different zone.
(I don't mean that availability is an issue, but rather, there are no *A flights between the two, and the only way possible is via other zone.)
I know that FF programs will usually not charge you more miles if flying eg FRA-BKK-HKG, even if FRA-BKK requires more miles than FRA-HKG, they will nevertheless charge you the lower (FRA-HKG) amount.