Here is a representation of how it works, looking down from the top. I have exaggerated for this discussion.
On the right is the filled in daggerboard and on the left...obviously the Gybing.
There is a fair amount of space, on each side, required for the Gybers which may lead to too much extra drag in the water also it tends to chew up the trailing edge. My daggerboard's trailing edges are being repaired right now.
While filling I left enough space in the back part, after filling, to allow the trailing edge to have plenty of room. I do not want the same problem again. The space is about equal to what Nacra does, since they started installing the boards fixed and not gybing. I have seen new boats with carpet and without carpet in that area but I do not think it matters if there is enough space so the trailing edge does not touch.