ATM the only option is to use /etc/skel and having the config copied on account creation time. but this is not really viable for distribution packages as you might have lots of old accounts where people switch their mailer. a nice option would be something like $(datadir)/claws-mail/skel which is copied to ~/.claws-mail when the directory is created. that way a distributor can e.g. enable the gpg/smime plugins by default.
In fact, this is already implemented: the contents of $(SYSCONFDIR)/skel/.claws-mail are used as a template on Claws Mail's first run, even if the user was created before that directory existed. I've tested with a minimal file containing only the plugins sections: colin@marv:~$ cat /usr/local/etc/skel/.claws-mail/clawsrc [Plugins_GTK2] /usr/local/lib/claws-mail/plugins/pgpcore.so /usr/local/lib/claws-mail/plugins/pgpmime.so (my SYSCONFIG being /usr/local/etc) What's written in the manual, section Deploying Claws Mail, applies :)