if you don't have the time to investigate, you can do this instead;
you can tell AO not to aggregate inline JS at all using the API (using the autoptimize_js_include_inline filter to be specific, see example code in autoptimize_helper.php_example).
and regarding;
Question - Is it advisable to use Autoptimize with Super Cache or other cache - or stand alone?
do use a page caching plugin, else AO is called on every request which could result in some time being lost.
frank