The CFP committee will rank teams regardless of whether they think that team will be a conference champion or not. It's a strict ranking of 1 through whatever number they rank down to (25?). Because a team is projected or likely to be a conference champion doesn't automatically get them ranked in the top 4. They get ranked where ever the committee thinks they should be ranked.

At the end of the seasons after the final rankings, the committee then takes the top 4 ranked conference champions and assign them the 1-4 seeds. The next 8 seeds (5-12) go to the highest ranked 7 or 8 teams left after the conference champions are seeded. 7 or 8 depends on whether the 5th ranked conference champion is ranked in the top 12.