I am sure the NFL is dismayed that there is some controversy generating buzz before the superbowl.
As far as refs knowing or not knowing, I am thinking this stuff is pretty common and the refs have always just went along with it. I mean every single ball but one where set up this way, presumably the one that wasn’t was for kicking. That doesn’t strike me as the procedure one would use if there is even a remote chance that the refs considered altering them too big a deal. Then a player complained, and like in baseball with a pitcher loading or scuffing balls only then do they start to take an interest.
Freegards
Not sure the league is that upset. They’re always trying to gin up stories for the long gap before the SB, and most of the stories are in the “yeah whatever” category some of which are pretty hilarious (Andrew Sharp’s article on Grantland is excellent). Yeah there’s the crowd of people that haven’t gotten over spygate insisting this is massive, but they hated the Pats anyway, and now they’re probably extra motivated to tune in and hope the Seahawks kill them. In the end it seems to be proving that all publicity is good publicity.