Even if it's from a magical source, soldier SS will absorb DoT as though it were physical damage (0 damage = damage absorbed by SS).

Funny side note: soldier SS won't absorb damage from a melee DPS limit break. It's not that LB busts through the SS and does damage, rather it completely bypasses the SS and deals full damage while leaving the soldier SS intact.

So magical DoTs are physical damage, and physical limit breaks are magical damage. The Allagans were a strange people.