And Fireball always does Xd6.
So what's actually the question here?
Ugly Scratch specifies the three things it overcomes. Just A Scratch isn't any of those things based on its current wording (regardless of actual intent for otherwise)
In its current incarnation, Just A Scratch is more akin to the ability of Swarms to reduce weapon damage based on how small the individual creatures in the Swarm are.
Ugly Scratch doesn't bypass that ability of Swarms either.