The reason they separated FBS and FCS in football was more of a safety issue than anything. Idaho St competes with BYU as well in football as they do in basketball, which is not at all. Yet you include them in one sport, but not the other? Simply because of a classification?
So if D2 got blended in with D1 in basketball then now being top 25 in basketball would be like being top 3 or 4 in football! We should do it! Of course D2 schools would have zero chance of winning or making the top 25 but we only care about sheer numbers in the classification.
In your scenario you are making Incarnate Word, Kennesaw St, Idaho St and 200 other nothing schools into BYU's equal. Talk about not a fair comparison.