In SD.IncidentManagement, open the CreateIncidentAdvanced model, and find the Send Notification component. Open that embedded model component, and edit the Send Email About Task Creation 2 component. Edit the To Addresses, and click the Add Single button, and select IncidentToCreate.SubmittedBy. This will add the submitter to the email that the affected user normally receives.
If you want the submitter to receive email with a different message, you can just copy the Send Email About Task Creation 2 component instead, and remove the primary contact from the to addresses and add the submitter. Then you can change the text of the email. If you do this, you will want to make sure you add error handling to catch any exceptions in the new send mail component. Just copy the Catch Error In Send Notification Rule and Create Log Entry components, changing the component to catch to your new mail component. You will also want to change the existing error handling to go to your send mail component instead of End, so it still tries to send an email to the submitter even if the email to the primary contact fails.