Autoptimize is a exelente wordpress plugin, but it seems it ignore the blacklist from "Exclude scripts from Autoptimize" option. The plugin persists to minify and combine, instead of leaving it as it is. So I found this filter, that I can check the url and check agains the blacklist. If the js item is blacklisted, Autoptimize will skip it.

Wordpress: Autoptimize, exclude js from combine and monification

<?php
// theme functions.php

add_filter('autoptimize_filter_js_minify_excluded', function ($condition, $url) {
	if (!$blacklist = get_option('autoptimize_js_exclude', false))
		return true;

	$blacklist = array_filter(array_map('trim', explode( ',', $blacklist)));

	return count(array_filter($blacklist, function ($match) use ($url) {
		return false !== strpos($url, $match);
	})) === 0;
}, PHP_INT_MAX, 2);

?>