Well, not really cut them off...
When I ordered my ATC Bobcat shell in late 2010, I really, really, disliked the black velcro showing on the side of the soft top material when the flaps were rolled up.
So, I asked Marty & Jeff if they could leave off outside rain flaps and the black velcro, and they said they could do that.
I was aware of the "special" bottom corners that FWC created to keep the rain out when the flaps were rolled up, and that ATC didn't do that process, however, I thought I'd take a chance on not getting rain into the camper with the outside flaps absent.
So, far I've gone through many trips where it rained, the top was up, and no water inside the camper.
A year or two later, I noticed that ATC was offering outside flaps that were removal-able, however, still had the black velcro.