This answer from Mike solved this (e.g. create a CGI process for this task):

[...]
So, yes, you can create a directory which it is then impossible to access --
this is an unfortunate side-effect of safe mode when PHP runs as an Apache
module and hence as the Apache user.  This is why hosted services often use
chrooted jails with PHP as a CGI -- the individual copies of PHP then run
with the appropriate uids of the host usernames.
[...]


Regards,
Summi

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