Atonement/spirits certainly are not breath type DMG. Hp modification aside, Breath dmg is subject to a magic acc check. Failing results in resists. 1/2, 1/4 and so on.

While mobs can have a static dmg reduction(rather misleadingly called resistance) against spirit DMG type , there's not a magic acc check, and normal magic resists do not occur.

The difference fairly clearly indicates a different dmg class than breaths.