Granted, most of what constitutes sports team fandom is illogical and irrational, but I think this might be especially so.
If you're an Alabama fan and spend your entire life hating Auburn, I don't know how you clear the logical hurdle towards rooting for them to win a BCS Title, just so you can claim a greater point on the supremacy of SEC football.
In CBB, I gave not a single fuck that Louisville won March Madness last season, in terms of how it reflected on Big East basketball. Can you imagine a fan of the Orioles rooting for the Yankees in the World Series, out of some sense of American League divisional pride?
To me, the difference that makes a difference is that no where else in this country is as insanely competitive as it is in the South w/r/t college football. And I think this "conference pride" business is a logical result of that.