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Message bar notifications can be hidden or set to go away automatically after 5 seconds (NoScript Options|Appearance)
Long awaited bookmarklets support. It allows JS on current page just for the bookmarklet execution lifespan. This technique should be safe enough, because JS execution in web page is strictly mono-threaded. Anyway, if you don't want or don't need it, you can turn on NoScript Options|Advanced|Forbid Bookmarklets.