I couldn't tell you. For aerial combos, I use j.BC dj.BAC, but that's only because the input is easier rather than using j.B, j.6B.
On paper, the damage is still the same. Not sure if the proration is, but it doesn't matter too much (imo) considering that the combo is pretty much over when you reach that point.
As far as that combo Rei listed, I'd say the reason why j.A is used is because of the pushout on hit is lessened, perhaps. That or just for ease of input.