Changing a (broken) email into another doesn't break anything. Changing
$wgServer could break several things, though.
http://www.mediawiki.org/wiki/Extension:New_User_Email_Notification
specifies:
$wgNewUserNotifSender
Email address of the sender of the email
Defaults to the value of $wgPasswordSender
(which we viewed, had www on it)
So you should set $wgNewUserNotifSender as the proper e-mail sender.
It's an extension parameter, so it won't break anything on MediaWiki.
Alternatively, you could set $wgPasswordSender before require_once(
"{$IP}/extensions/NewUserNotif/NewUserNotif.php" ) and let it set
$wgNewUserNotifSender by copying it.