This happens to me to. And no matter what I select for "Max. Allowed Cronjob types (chrooted and full implies url)". I can see that all those additional folders get created when I add shell user. Not before. How can I disable creating all those folders? When I was at another provider and had reseller account I didn't had those problems. It was version 184.108.40.206 and now I have 3.0.4.
Any ideas how to disable creating all those folders?