Looking at the Articles code, it appears to save a single new resource directly without invoking any events or calling any MODX processors (though I don't have the current version installed, so that may have changed).
That would explain why the System Setting has no effect.
IIRC, there used to be a System Setting OnSaveResource or OnResourceSave that you could connect a plugin to, but I don't find it any more (if it ever existed) so there may be no way to solve this without hacking the Articles code.
Changing this line in the articles.class.php file:
if (!$newResource->save()) {
to this:
$this->set('published', true);
if (!$newResource->save()) {
would certainly do it.