Path in external JS

[Kolyok]

Maybe not the best solution but you could try to declare a javascript variable just before loading the config.js and then pass that variable to prefix.

PHP Code:

#Set variable before loading the config.js (inside your template file)

var ThemeStyleAbsPath = '<?php get_theme_url(); ?>';

#Pass variable to config.js

window._skel_config = {
    preset: 'standard',
    prefix: ThemeStyleAbsPath + '/css/style',
    resetCSS: true
};