I use the Topeak MTX trunk with the integrated panniers and have at least one filled up 1-2 times a week. I didn't mind losing the forward pannier hook since I never used it anyway. I tend to hit the pannier with my heal if I have it too far forward. There is enough clearance between the rack and disc brake mount to allow for a real pannier hook though.

Of course this is a custom setup where I had to bend the rack to make it fit like I wanted it to. Without the bending it would have sat up a few inches higher but both of the pannier mounts would have been preserved.