I think partly to clear the valve cover/head for a larger diameter distributor cap. The pertronix distributor uses a larger diameter cap (than stock) and short shaft similar to stock length and you have to dent or grind a spot on the valve cover for it to fit on the big block. Also, two different shaft lengths for B-Block vs RB- Block so maybe it is also for MSD to easily switch shafts depending on the application/order.
I read a long time ago that Dick Landy lent a hand in the development of the dual plug 426 hemi heads.... I could be wrong on that.....