Yes it can, what are you talking about? it's a file in my home directory owned by my user, the same which is running claude. In fact it did edit it for other changes. And I was already in bypass permissions mode. I wanted to change the default for new threads.
The harness runs itself in a sandbox, Codex does the same. Then it can request approval for individual tool calls to be made outside that sandbox, depending on your permission mode. At least this is the case in MacOS.
I see what you mean now though - you can change the default permission mode with /config in CC, but it will indeed not make that change on your behalf.