I've seen several times where he has flinched as if about to run, then chose instead to stay put.

The only interpretation of all this (and other things harder to describe in 500 characters) that makes sense to me is that this cat has confirmed to his satisfaction that I am indeed a safe person, knows intellectually that I will not hurt him, and is trying to retrain his own reactions, push his comfort zone, so he isn't controlled by his PTSD triggers.