Would it be possible incorporate PortableApps.com AppCompacter into PortableApps.com Installer? I think that would help streamline the app creation process.
Maybe the installer could look to see if AppCompacter is installed, then offer to run it before creating the installer (and passing the selected directory to AppCompacter).
It's best to run AppCompactor first, then test the app out to make sure it works compressed before packaging it in an installer.
Sometimes, the impossible can become possible, if you're awesome!