After a entire night I’ve get the answer.
Reflecting on why the customizer showing me the widget areas only through the wp_footer hook I have checked my footer.php and the problem was that wp_footer() were called before the sidebar section.
/* Always have wp_footer() just before the closing </body>
* tag of your theme, or you will break many plugins, which
* generally use this hook to reference JavaScript files.
*/
wp_footer();
Moving it after sidebars all works perfectly.
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