Frank Goossens on "[Plugin: Autoptimize] Does cdn help with large file?"

no, because W3TC would empty the CDN-cache, but not the cache on your origin server.

instead try to exclude the page specific JS (cfr. that blogpost) or alternatively add the PHP code to tell AO not to aggregate inline JS (similar to the one you added not to optimize inline CSS), cfr. autoptimize_helper.php_example;

add_filter('autoptimize_js_include_inline','ruddyred_ao_js_include_inline',10,1);
function ruddyred_ao_js_include_inline() {
	return false;
	}

frank