Don't forget about the rack itself in making this decision.
I learned the hard way why you need three rack legs with panniers. It's to keep them out of the spokes. My lesson was served up while using nice, stiff-backed panniers too. Even so, they swayed into the spokes. This was neither fun nor pretty.
Roll-up panniers would seem to be even more likely to sway into the spokes without sufficient rack legs to keep them out.
To the main question, my preference is for a separate trunk bag and panniers.