Zoe's E Doesn't Actually Do True Damage
I have been saying this over and over since her numbers were spoiled. The "True damage" portion of her E is based on damage that was reduced by resistances. If you take the full proc it means that you took damage that did at least that much through your resistances and so the doubled damage is just straight doubled, instead of being doubled and reduced again. If the second proc WASN'T true damage then you'd be running into a case where resistances were actually being more effective than they should be. The damage type is set up to basically mimic the damage type of whatever procced it without getting reduced by resistances twice.
Tl;dr If it wasn't true damage than resistances would come into play twice against the damage, so stop complaining about it.