So there needs to be some clarification regarding FBS and FCS schools. Can a FBS school play a FCS school? Yes. The term D1 has been basically changed from the past. Texas State for example, they played in the semi-finals in 2005/2006. They were FCS. They had a playoff system in place just like D2.
FBS were schools that were in the bowl system, aka the BCS bowl games (think UT 2005/2006 championship vs USC.
So they are separated. However, I will add, they have given D1 status to a lot of schools that used to be FCS. Texas State, UTSA, App St, Coastal Carolina, etc.
So yes there were 2 champions. One for FBS and one for FCS. FCS used to be D1AA. Again they have been doing the playoff system for a long time now. This will be the first year for a real playoff in D1 FBS, since there is a playoff bracket now.
Long story short, there is a difference between FBS and FCS even though you can say FCS is D1. Call it power 5 or whatever you want. So yes there was one true champion for FBS, FCS, D2, D3, etc. You can agree to disagree but that's the truth.