If you want to use OSGI (eg. in Eclipse RCP) then it is impossible to obfuscate (change or flattern) package names.
OSGI configuration in META-INF/MANIFEST.MF contains Export-Package entry with exported package names usable in depend bundles.
Export-Package: com.app.data, com.app.service
ProGuard is unfortunately not able to modify package names in these resource files.
It would be nice to scan and replace package names in the specified resources (configuration files).