Officials have an incentive to be biased in favor of the teams from the conference that employs them because:

(1) the prestige of their employment is tied to the success of the conference that employs them;
(2) they will face coaches, players, and fans from the conference that employs them on an ongoing basis, while they will face the particular coaches, players, and fans from a particular out-of-conference school much more rarely; and
(3) they are likely to become partial to, or even fans of, the teams with which they are most familiar and/or from the region where they are from, grew up, attended school, etc., etc.

More broadly: (1) officials are only human, (2) humans are beset by all kinds of cognitive fallacies and distortions (e.g., selection bias, hindsight bias, etc., etc.), and (3) sometimes officials can't help but be influenced by who they are, where they come from, the people they interact with most, and who signs their paychecks.

I suspect there's something to all of this, but I'm not super worried about it. I think officials generally do a good job, and that things like their appreciation for the game, their desire to be fair, their desire not to look dumb on TV, and their desire to continue to be gainfully employed can generally counteract biasing influences. On the other hand, I think it's dumb for officials to be employed by the conferences. The NCAA should employ them, train them to call games the same, dispatch them to games somewhat randomly, etc.