I am trying Wix 3.6 and this is how it looks right now :
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You could add in a reference to the WixUtilExtension.dll to the installer project, then use XmlFile to update the app.config like:
Note that you'll need to set the directory and the name of the .config file (you could just use $(var.ProjectName.TargetFileName).config which should work it out for you automatically