I believe it’s because the WKA is recognized as the official United States liason to the CIK-FIA; like ACCUS is to the FIA when it comes to car racing.
Since the KZ2 class at the SuperNats is officially scheduled CIK calendar (at least I think it is), a CIK license is needed to compete in it. So, since the WKA is the American contact to the CIK, they would process all applications for CIK licenses. Despite the WKA not holding a KZ shifter race in years.
Whoops, nevermind. David pretty much explained it already.