We don't know why Android Auto isn't smart enough to know that Pulse SMS is the default SMS app, but the two notifications you see are: one from Pulse SMS and one from Android Auto's internal SMS integration.
To just get notifications from Pulse SMS, simply turn off the SMS permission for Android Auto by opening your system settings, finding Android Auto in the installed apps list, and disabling the SMS permission.
You will now only receive messages from Pulse SMS, when they arrive.
