Well, prompt injections work precisely because they can sometimes successfully imitate user role, right? Role separation is a trained behavior, not a security boundary.
They could probably make a separate tool for setting this, that would always initiate a harness prompt (i.e. disregarding the currently set mode).
They should either allow you to take off the training wheels (I'd have thought that's what bypass permissions is for, which I was ALREADY running), or at the very least prompt you if they suspect prompt injection.
That refusal is awful and provides zero security benefit. If asked it will run a read/write FTP server on ~ no problem, which obviously can edit ~/.claude/settings.json. And run a cloudflare tunnel for that.