The .service files aren't config files. It's just that some packagers plunk hard-coded settings into the .service file when they should make them configurable. e.g. redhat/centos hardcode "PrivateTmp=true" into the .service file for apache httpd.
So instead of
[Service] ExecStart=/usr/sbin/mydaemon -s 03:00:00 PrivateTmp=trueIt should be
[Service] EnvironmentFile=/etc/sysconfig/mydaemon ExecStart=/usr/sbin/mydaemon -s $STARTTIME PrivateTmp=$USEPRIVATETMPThen all tweakable settings go in /etc/sysconfig/mydaemon instead of the .service file. (or /etc/default or whatever)