Thanks for reporting this, Grahamw81. If you have confirmed that you are getting the data that you expect, that is what matters. I'll report to the dev team that the message should take into account that inputs may be configured directly through the add-on.
To clear the message, you can try going to the configuration tab in the Splunk App for AWS, opening your inputs there, and resaving them without (necessarily) making any changes. Try this first with just the Metadata input or the Billing input to see if that changes the message. If that works, you may want to also resave your Config, CloudWatch, and CloudTrail inputs from the app. NOTE, however, that resaving CloudWatch, CloudTrail, and Config inputs from the Splunk App for AWS may cause some of advanced parameters to change when you resave. See http://docs.splunk.com/Documentation/AWS/4.0.0/Installation/Migrationguide#Migrate_your_existing_inp... for details of the resaving behavior. You can always change the parameters back from the add-on if this affects you.
