Hello!
I have the same problem, and after some hours spent to find the right setting, I finished to dig into the code, and I found the following code, into the function " function postMessage($vars, $origin='', $alerts=true)" :
if ($autorespond && $alerts
&& $cfg && $cfg->notifyCollabsONNewMessage()
&& strcasecmp($origin, 'email')) {
//when user replies, this is where collabs notified
$this->notifyCollaborators($message, array('signature' => ''));
}
We can see there is a condition, which prevent notify collaborators if the message come from email, so in my opinion, you can configure all you want, the code will always prevent sending notifications to collaborator if the message come from email...