Is there a way to enable shortcodes in text saved in the customizer and retrieved using get_theme_mod?
I'm guessing there's a filter in a similar manner to enabling shortcodes in widgets.
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To enable shortcodes in text widgets add a filter like that:
add_filter( 'widget_text', 'do_shortcode' );
You can pass every string to
echo do_shortcode( get_theme_mod( 'theme_setting' ) );