There is no policy or standard for the preferred method to create certain directories and permissions.

I personally think its better to setup permissions once using make_dirs or the INSTALL script.
First reason is that if the service fails and the run script runs every second its just a waste of time.
Second reason is that if the admin changes some permissions some services tend to just blindly recursively chown or chmod directories making it impossible to setup different permissions without
changing the run script.

Directories on tmpfs are an exception.

#571
#5