I don’t know why they changed it from 5 to 3%. However, i could think of a reason why they would lower or remove it at all : With the old atk-def damage system a boss having, say, 10k defense would lower the damage alot while this pseudo-def-ignore effect would counter that.
If however you have your damage formula changed so extremely high def values are less effective than before (which it is with the new log-formula, if i remember correctly) but you keep the old increase-damage-directly-based-on-def bonuses the way they are (which QS- and Fencer-skills seemingly are since they probably simply forgot to adapt them to the new log-based damage formula) then over time, with bosses getting thousands and thousands of more def to counter the power creep of equipment, these ignore-def bonuses would become extremely powerful.
This, however, is just my reasoning for why they could’ve done this change.