Frank Goossens on "[Plugin: Autoptimize] Clear cache without saving changes"

well;
1. autoptimize only caches CSS/JS
2. if you don't have a page caching solution (plugin), autoptimize gets called every time, but will check if the aggregated CSS/JS is already in cache and return the cached one if so
3. if you have a page cache and the requested page is in cache, autoptimize does not get called at all, as the page cache will contain references to the already cached optimized CSS/JS

so it actually depends on your page caching solution, really :-)