You need to digitally sign your Adobe Air application. Inorder to remove the unknown publisher. There is nothing to do with the app-xml file or coding with that.
By digitally signing means you need to purchase a valid license certificate from recognized company's such as Verisign and Thawte etc;...
So that to show customers that your code and content(Application) is safe to download
You can find more information on this checking the below links:
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