I think a general mechanism that allowed you to set default command-line flags would be useful. (And of course you'd need a new flag to skip that.)
For example, a new [commandline] section, where command-flag is the key or command-flag.1, command-flag.2 for repeated instances. /r$ -- Principal Security Engineer Akamai Technologies, Cambridge, MA IM: rs...@jabber.me; Twitter: RichSalz