Is it possible to tell Eclipse to use some extra arguments for aapt (-0 in specific)?
I have been looking for past couple of hours and the best hack I came up with was to create a wrapper for the aapt tool to inject the argument to the command line. The trouble with this approach is that whenever I should lose that wrapper, then I'll be quietly introducing a bug into my application.
I don't think it is possible without some sort of wrapper script as you mention.
Alternatively, you could use an Android ant script to build the release version of your application, as that lets you easily override the command line parameters used. It also helps you build things independently of the Eclipse plugin which is useful should you get into continuous integration.
Hopefully you wouldn't be quietly introducing a bug anyway due to at least smoke testing your app before release.