Bene and HG are intentionally delayed because they're extremely powerful and allow you to avoid certain mechanics. For balance, they were given slight delays. Other skills like Disembowel, and Bio apply their debuffs at the end of the animation rather than the start. I believe any skill without a cast-time has this penalty intentionally since skills like Bio and Benediction can be cast while moving and are instant (no cast time) and can't be interrupted.