Hmm something's up here. This is from their FAQ,
BakFlip Tonneau Cover - Installation a little more than half way down the page:
Does this cover work with "flip out" Bed Extenders that flip over onto the tailgate?
Absolutely! The cover works with all Bed Extenders.
---------- Post added at 03:07 PM ---------- Previous post was at 03:06 PM ----------
But a little googling shows this:
Bakflip Drainage Tube Fix For Bed Extender - Ford F150 Forum
Those pics tell me if you tried to rotate the extender out, you'd be right into that drainage tube. Does this guy's fix solve that issue? Not sure...