W3Total cache doesn't handle Jquery

If set in auto and try to use any of the Non-Blocking options this plugin break the site, disabling any feature that uses Jquery.
I’ve seen the plugin author recommend to disable auto and use Manual mode, but then you have to specify every single js from the theme (that could be a lot). Also to do the same avery time you update a plugin or theme.

Would be possible for the plugin author to include a text area in the minify options where to put the js you need to load before anything else the same that there is a box to specify the js you don’t need to minify??

I’ve seen a lot of people is having a lot of trouble with Jquery and W3total cache, and actually that library is widely used…. I’ve tried to put the Jquery at the head, it doesn’t matter, w3 total cache inserts its cache file before.

https://wordpress.org/plugins/w3-total-cache/