I'm pretty sure that if you want to use Flagellents to expand, you want to use a small squad of Men-At-Arms in front set to Hold and Attack, with the Flags to the side and just behind, set to Attack Closest/Rear. This way all enemies (specifically missiles) will target the guys with heavy armor and shields, while the crazy Flailers run in and smash everything. Though, I'd think that with a proper strategy, they'd actually come into their own later, against your human neighbors.
That said, I tried a test some time ago using mostly Flags (I think I did the F9/W9), and I won pretty much all my indie fights, with such high losses that I had to reinforce for the next attack.
Bearing in mind this was before I really understood the math behind shields, etc etc, so they had no blockers.
