In my example it is already there. This script includes tabbed widgets, some slider and other miscellaneous stuff, normally located in the head placed by the themes author. Unfortunately it only works if I add it to the ignored scripts in autoptimize settings and if the other scripts, here combined and minified by autoptimize, are loaded(?) before.
But there could be tons of other reasons to define the place where autoptimze output its awesome job even for the css output. And in my first suggestion I didn't consider that simple HTML comments like <!--AutoptimzeJS--> as optional alternate tags to define that output places would exactly do what I was searching for. Sorry for the wall of text.