Yup, its due to the way the effect is applied by script, and its part of the EffectDamageIncrease() script function, the full details of what it does for damage types here;
https://nwn.fandom.com/wiki/Damage_increaseThere are a lot of spells, feats and effects that apply bonus damage in ways it empowers the character, not the weapon, and there isn't a clean way to change how the damage is treated. Damage could be applied to weapons only but what if people are disarmed? They still need the buff. What if they are wearing bracers instead of gauntlets? No gloves? Creature form doesnt use a proper creature weapon? Creature form actually uses a weapon? Damage types no longer stacking so certain "builds" or weapons become redundant?
Its a large amount of IF checks that ultimately could be applied to every spell and effect and any change in variables such as switching weapons would have to be accounted for...
.. or we can just have one line of EffectDamageIncrease() left the way it is since applying to a character over a weapon resolves all the situations a character should have the damage, and just be aware that there is a damage resistance bypass quirk that can't be resolved in any efficient or timely manner.