I don’t use AutoUpdater. I wrote a similar tool, Molu Update Server, circa 2007 that handles all update tasks except replacing the Omnis engine itself. Omnis Studio 10 has an option of running a script at launch, which promises to ease the update process.
The challenge of writing to the xcomps directory is the access permissions enforced by the operating system. I am using an iPad at the moment so I cannot verify this, but any file that is put into the “first run” target directory in the user application support area should be writable by an Omnis app or external app designed to update your application.