As a PyroLinkerThauma, I don’t think the problem itself lies on Joint Penalty, since as of current, it only doubles AoE damage, by doing a tick of damage from the AoE skill, and other tick from Joint Penalty.
It used to multiply the damage by linked enemies after the merge, but it was patched not too long ago, if I recall correctly.
But the problem appears when you consider how the “Magic Missile” bounces, I think it works considering AoE defense of the enemies, and that’s why it deals so much damage after you use Hangsman’s Knot, and that effect can also be done with Falconer’s Circling.
I notice this is the current effect since my Fireball is not as strong as before a recent patch, where I could easily kill 80k+ mobs with a single fireball, this no longer being the case now.