Because there are so many bowls. There are 32 bowls so 64 FBS teams are needed to fill the slots. An FBS team needs 6 wins to be bowl eligible.

I just did a quick count for 2006. I counted 56 I-A teams that managed at least 6 wins without needing a win over a I-AA to get there. I might have been a little off on my count because I just went through it once. But it's pretty clear that there would be a substantial risk that there wouldn't be enough 6 win FBS teams to fill all 64 bowl slots without games between the two subdivisions.