Comment by Ekaros
One reason I could see is to keep perceived price level for the frequent flyers. If they don't see best deals they won't expect those. And the hardcore deal hunters are not loyal to you or your brand.
Giving frequent flyers very good deals make them expect them, thus not be so willing to pay "regular" price.
They could easily position it as a reward for loyalty for FFs who spent more than $X in the last calendar year with them.
The loyalty reward in this case would be treating virtual interlining tickets as if they were an actual interlined ticket.