Their regeneration is stated as contingent on proximity to allies, so the apparent intent was that players would have to be pulling them apart from the swarm and killing them one at a time (like what you do in Shroud2). If you weren't meant to be killing them, why would the devs have bothered to give them a situational vulnerability, and not just made them ultra-regenerating at all times?
I suspect the goal was that you'd need to send away around half the party to work on killing the shadowfiends, which would more than double the time spent killing the boss. Since the current time to kill him is weirdly low, it would make sense it was supposed to be slower.