> So, How I can disable the creation of that garbage from my .emacs.d
> directory?

    (setq org-persist-disable-when-emacs-Q t)
    (defun tv/advice--org-persist (old-fn &rest args)
      (let (user-init-file)
        (apply old-fn args)))
    (advice-add 'org-persist-write :around #'tv/advice--org-persist)
    (advice-add 'org-persist-read :around #'tv/advice--org-persist)
    (advice-add 'org-persist-gc :around #'tv/advice--org-persist)))

-- 
Thierry