One thing does come to mind and that is that if you purchased a 440 (or bigger) car w/4-spd, the Dana axle was std. It could be they didn't want to go through the expense of tooling another differential for the 69 440 a-bodies. So it was offered with Auto only.. It did come in the 68 Hemi cars w/4-spd, but that was it..
Whether it was a 440 or a hemi if you wanted a 4spd you had to take a dana. And yes you had to pay for it when it comes to B bodies. I my self, I am going to run my 4spd, 8 3/4 with a 496ci. 383 in my 69 barracuda.