1 minute Workaround *
My scenario is mini cart shortcode not rendered in FSE header template , while its working good in all other places in site.

-in site editor create new template part, choose general in the part type and name it , in my example I named it : mini cart icon.
-in the new template part insert your shortcode and save.
-go to the header template where the shortcode not renderd, remove short code, and insert template part element , choose the template part you just created in my case ” mini cart icon” , save.
-result: shortcode rendered in the frontend correctly .