FWIW, Pat Kirwan and Jim Miller were talking about this on Sirius NFL yesterday and basically said "nothing to see here."
Their take was that the QB and refs are talking the entire game (as is the MLB on the D side) about what they're going to do, things to watch out for, etc. and that it's just not that out of the ordinary for a ref to give a congrats, or good game, or butt pat (their words) after a game. Add in the fact the some of the refs and long term players have known each other for many years, and it's really not that odd. Bad optics maybe, but not conspiracy level stuff...