I would compress them alone for the simple fact that it prevents them from ever bulging (which bulging can also cause stretch pressure on the bus bars and cell terminal mounting bosses later as the cells start to push apart).
And especially for mobile applications, where there is shock/vibration involved, I would only want them clamped so the cells can't wiggle around and cause more stress on the bus bar mounting bosses...
A clamp assembly also makes it easier to move around the battery if needed (when not in a box). Holds them all as one tight unit. You can still put that into a box as well of course.