I was able to override the multi-site notification email by adding these:
remove_filter('wpmu_signup_user_notification_email','admin_created_user_email');
add_filter('wpmu_signup_user_notification_email',<function_name_here>);
add_filter('wpmu_signup_user_notification',<function_name_here>);
add_filter('wpmu_signup_user_notification_subject',<function_name_here>);
Adding the three filters at bottom i.e. email,notification and subject allows you to override the content and the subject of the email.
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