These sorts of anomalies are rare. They tend to form in the early part of the marking season (due to only a handful of games being involved for a referee) but by the end, a pretty accurate picture is taken. The other reason this can happen is that a referee is officiating differently when NOT being assessed, but has not clicked that by doing that (e.g. by not cautioning to 'do a club a favour') they are damaging themselves in the eyes of the clubs.
As an example, I was 4th man on a game where a referee did the classic "Give a corner / Oops it's clearly not a corner / Find a free kick to the defence". It was very obvious. Did either club thank him for it? No. Both managers were chatting on the touchline and saying to each other that they were going to mark him down as a result.
Club marks do involve the whole package, which is why the FA have a "Manage the event" coaching theme in the senior game. I would never say you have to nod and agree in the boardroom. However, being open and honest is the way to go. When I've listened to clubs talking about the infamous "last week's referee" it is generally NOT about decisions (penalties and the like) but tends to be things like: "He was arrogant", "We couldn't talk to him", "He wouldn't admit he was wrong". You don't have to admit you were wrong if you genuinely don't believe that, but empathy for the club point of view is essential.
