Shadowtrap and vaulthunter.exe seem to be connected to each-other. When you go inside the VH.EXE thing in clappys subconscious, you get to see a flashback with jack activating fragtrap for the first time. The first voice seemed to be shadowtraps, then it bugged out and clappy came back. That was probably when shadowtrap got thrown into quarantine, leaving clappy with a new ability that it cant fully use without the modification that knew how to use it properly.
I think a key difference that i just realized is that Shadowtrap isnt’t a Vault Hunter or Warrior unto himself, just rather the manifestation of the deadliest and most stable version of VAULTHUNTER.EXE itself.
Fraggy has the “flawed” EXE but it is these “flaws” that allow him to win out versus the “perfect” but set in its way and unable to adapt Shadowtrap EXE code.
It’s actually much like the difference between Humans and Machines; machines are cold, impersonal, seeking only perfection.
Humans realize that their true strength and value lies in the fact that they are flawed but able to feel love, empathy, pity, mercy, compassion, which allow them to overcome seemingly insurmountable obstacles and limitations.