Yes, I think it's as expected. The whole Script Blocker thing is quite a hack, and I think this was needed to intercept Netscape scripting.
As for why it's so even when the option is unchecked... I'd say so that if you check the option again, you won't have to restart the browser for the change to take effect, but even the already running instances start to be protected immediatelly.
(But it's just my guess, I don't know this module very well.)
Don't have answers for the other questions... yet.