How about instead of making a binary choice of add damage or not on nanos, perks and DoT's you make it a 0-x% range, allowing benefits from add damage to range from nothing to maybe even a multiple ( greater than 1) of your add damage score, this would make it so that for example DoT's could get a 20% benefit on the tick or even less, in addition Tripplors and other multi hit nukes might be better balanced by not adding a full amount on each hit.
Ok, so maybe tripples aint making it into the new system but the point still stands.