Just want to add some small things, about the blessing option.
flagelants have 2 attacks with there flails, meaning that they benefit alot from a offensive blessing boost, (fire in particular)
Luckely for game balance they really need a defensive boost as they are very fragile.
But since the simply are the sacred trop benefiting most from a fire blessing at all I asume that its a good choice
As blessed flagelants have very good morale, they don't need to be hoarded in big squads comparede to other units. This can be used togethere with small lines of Marignons decent heavy infantery in the front to suck up(defleckt) the intial charge. And then flagelants making an hard hitting counter attack.
Small arrangement like this can cut alot down on the causalitys. But the key is to use the heavy inf as well
if you bring crossbows they will result in frindly fire losses, but as they are slow shooting and armour piercing, you still want it to be crossbows and not normal shortbows (from a conqeurred indy) there are bLasting your flaggelants. It takes good judgement or experience to know when to bring /and not bring archers/crosbows. Sometimes you don't wan't to bring the flags as the heavy inf/archery combo is simple better suited for the job.
By the way I have a question ? is there any advantage to use flaming arrows spell on crossbows than on shortbows? The question is does the flames be treated as a seperate attack or is it benefiting from the crossbows armourpierce?