You could change this code around line 315 of the StageCoach plugin:
/* duplicate and save the staged Resource */
$stagedResource = $resource->duplicate($params);
$stagedResource->save();
to this:
/* duplicate and save the staged Resource */
$stagedResource = $resource->duplicate($params);
if ($stagedResource->get('class_key') == 'Article') {
$stagedResource->set('show_in_tree', true);
}
$stagedResource->save();
I'm pretty sure, though, that when you hit the stage date, the real article will show in the tree. I think you could fix that by changing this code around line 190:
$success = $originalResource->save(0);
to this:
if ($originalResource->get('class_key') == 'Article') {
$originalResource->set('show_in_tree', false);
}
$success = $originalResource->save(0);
Let me know if it works. If it does, I'll add it to the next release.