This is a good point, although I'm not quite sure what to do with it.
Before the idiotic conference realignment, there was a regular season, the second half of which in conference games, and the NCAA tournament was a way to find out the best overall teams among all the conferences. It would be very discouraging to be the second or third best team in a conference, go through an entire season, get invited to the tournament, and then find yourself replaying a conference opponent you've already played and lost to during the regular season.
The selection committee understandably decided to keep theseunfortunate meet ups to a minimum, resulting in the current rules. However, those rules will put together when it was not likely that nine or 11, or 12 members of the same conference would be in the season-ending tournament.
While you still might have the same desire to play somebody other than a conference team, it becomes much tougher to slot all those teams and avoid meet ups without creating the potential of unfair slotting of one of the teams without so many conference members in the tournament. The unfairness of having to meet a conference following an early round needs to be balanced against the possibility that a team is moved away from the natural spot, either seed or region or both simply because there are so many members of a single conference.
The ideal situation would be to rethink the stupidity of the conference makeups but I recognize the folly of tilting at that windmill, so maybe the conference meet up rules need to be relaxed.
Which ever is done, it's one more black black mark on the conference realignment debacle