Yep. I figured this out some time after I started to play the game over a year ago. I was wondering if Crushing Verdict increases damage on acid Judgment. Sure enough, investing 1 point did increase its damage very slightly, so additive nature of % damage on skill’s nodes was obvious.
Actually, I’m pretty sure by game mechanics those % damage bonuses indeed do convert, it’s just we don’t see any change in tooltips. Like, for example, piercing damage on Rending Force remains piercing despite us having full Justice set.