Permissions set too soon by init.sh

[starchy]

my_init runs /etc/my_init.d/10_init.sh, which set file permissions in the drupal directories, before bringing up apache. After those permissions are set apache/drupal/OA creates new files and sometimes rewrites files under /var/www/html, which leads to errors in the UI like

Warning: file_put_contents(private:///.htaccess): failed to open stream: "DrupalPrivateStreamWrapper::stream_open" call failed in file_create_htaccess() (line 496 of /var/www/html/includes/file.inc).

(I can see this isn't being actively developed, but github doesn't seem to allow me to open the issue against my fork right now)