All teams are ranked. Then the highest four ranked conference champions get seeds 1-4, and the next 8 highest ranked teams get 5-12. So yes, BYU could be ranked 9 at the end, but then get a 4 seed. Seeding only comes after conference championship games, after the final ranking.

See https://www.ncaa.com/news/football/article/2024-08-29/how-12-team-college-football-playoff-will-work-teams-schedule-bids?amp