Atonement is iffy, I did some random tests a while back and it's like weird hybrid damage. It may have a breath component to it(i.e 50% of its total damage) which is why it's capped at like 360ish damage on things that resist breath damage heavily. Ok so I guess this adds veracity to my claim that there's no such thing as 'spirit damage', they're simply non-elemental breaths.
HP is usually the modifier for breaths but as you stated Chi Blast might be an exception. I think they just slapped a heavy BDT on new NMs since WoTG because they preemptively quelled any chances of the player community relying on weak yet extremely consistent and accurate attacks to wittle down NMs. Breaths are special in that they bypass MDT/MDB/INT and MND as well as level correction which gives them a unique advantage. Though the player base never really exploited them due to their rarity...unless you count 2003 Spirits Within spam. It's a shame they implemeneted a universal BDT on all new NMs because it would have given BLUs a unique niche for dealing decent damage against NMs in Legion or Voidwatch to be able to stock up on HP gear and deal highly consistant damage with the various breath spells they own,while also justifying all of the "Enhances Breath" armor they can use. Would also make Dragoon more worthwhile since the post-WS breaths that our Wyverns use would deal 200-350 instead of 20-30, which would technically count as enhances our WS# by 200-350 if you add it to the DRG's parse