Actually, I think both of your points may be in play. 

Civil Comments enforces a pre-conceived standard through their unpublished 'algorithm' which removes comments supposedly based only on the responses of others in the community.

To believe that, you have to also believe that comments submitted, published and even responded to, are removed by subsequent flags only.   

You also have to believe that comments are submitted and an unknown number of 'uncivil' or negative reviews (as determined, once again by the unpublished 'algorithm') prevent publication in the first place.  

I have personally submitted comments which were purportedly 'rejected as uncivil' and 'removed as uncivil'.

I have reposted both kinds on several occasions and the subsequent post has NEVER been 'rejected' or 'removed'.

Without publication of the respective 'algorithms'  to someone with the ability to analyze and decipher them, we are left  with out own suspicions and biases.