I would say conference champs should get an auto bid, but with the amount of teams that are in the playoffs, if you win your conference, you'll be in.
The issue with seeding conference champs a special way, is that just about every conference is a split, and some of them span across three classifications. So how would you determine conference champs for seeding? Before it was top three conference finish OR .500+ win percentage. Now with conferences spanning three classifications, lets say there are 6 teams in the conference. Two of them are 3A, two are 4A, & 2 are 5A. The 3A team finishes 4th in conference and has a 4-6 record. Do you seed them with conference champs? Is it fair not to, when they play in a conference that has over 50% of the teams in higher classifications?
I think the NCHSAA messed a lot up when they went to 8 classifications.