Yes, it is organizer's decision to allow non-certified judges over certified judges. I have competed in contests before where the organizer purposefully limited the number of CBJs to allow judges from local businesses because she was with the chamber of commerce and these businesses were her sponsors.
At my contest, we give priority to CBJs because that is what our teams expect. I have had to use a few non CBJs before but it was only because of last minute cancellations (day of contest). Our rep does assign seats at the tables based on the list that we've given him a few days before the contest and our judging coordinator plus the rep make sure everybody on the list is seated.
My suggestion is when you check in at your next contest, make sure to introduce yourself to the rep(s) and the organizer and hopefully they remember you when time comes to be seated. It would be nice if all the reps would do pre-seating of judges a lot more. I had to stand in the rain at a contest earlier this year along with about 40 other judges due to sorting by experience. Probably won't go back to that contest again if the same reps are there.
Hope this helps.
Fort Smith Barbeque Society