You lose out on full control of ignition timing for both leading and trailing if you don't use msns-extra.
If you're going to use msns-extra, and you're going to modify your ignition system, I'd just let msns-extra control ignition.
Also, getting an MSD boost retard box along with a megasquirt 1 with a v3 board will most likely cost more than just getting a megasquirt with an msns-extra board.
Boost retard boxes as far as I know also aren't rotary specific. None of them will retard trailing ignition when you retard leading... which means you could get trailing firing before leading which is bad on a boosted rotary from what I'm told.