If it's the same script (as in it has the same name e.g script.js) then it's just how it works. It's updated anywhere it's used. When you think about it doesn't make sense to do it any other way.
My issue with the Editor is that it seems it is now impossible to refresh script attributes from locally hosted code. The Designer let's you do it (somewhat) if you know how to bypass same origin policy but with the Editor it's not possible at all - there's just no button for it. Ideally CORS or JSONP (whatever is easier for you to implement - trivial either way) should be used to retrieve and run the scripts from localhost.
Also wanted to point out that I think the Editor looks fantastic. Great job overall, slick look, feels faster all around. I like it a lot.