It's mostly just a mechanical thing - everything that is not a weapon skill (disabled by atrophy) is a spell (disabled by silence). I guess some of the skills you listed could be moved to be affected by atrophy instead, but imo it's not the most critical issue.
Also, a lot of these skills like cloak and dagger or phoenix dive don't look like something you can do without magic really. Some fantasy settings try to portray these as exceptional feats but jumping 15m without magic doesn't look convincing at all to me.
The only skill that shouldn't be subject to being disabled by CC is Break the Shackles imo (which I would prefer to be usable vs hard CC as well, that would make it competitive vs dome of protection and time warp)
Last edited by MadDemiurg; 28/10/17 11:07 AM.