My guess is that mortar trap in particular, and any similar skill tagged as “scales off player damage bonuses” which deals phys damage, will benefit from the IEE damage conversion.
AFAIK skills like Mortar are considered likely as “totems”, hence share all, with no exceptions, damage modifiers innate to the player.
But in relation to certain game mechanics and rules, some modifiers may not apply - for ex. flat damage when there’s no %WD. Or ADCTH, or RR, or any mechanic which requires WD to work.
But conversions IMO should. IEE doesn’t add “additional extra damage of an element” when converting, it just partially converts one to another.
In my opinion, mortar will benefit from the conversion (as skill has phys damage portion), wouldn’t gain the flat elemental damage from IEE.
May be wrong, though. Don’t count on it.