packager uses jlink API to create an image from a given modulepath and root modules.

--installed-modules plugin is enabled by default and there is no option to disable it.

Packager has to explicitly include this plugin in their implementation; otherwise it fails to create the image:
 plugins.add(Jlink.newPlugin("installed-modules", Collections.emptyMap(), null));

The default set of the plugins running via jlink command-line should be the same as running it programmatically. It seems that the current implementation has no plugin selected if called via jlink API. This should be revisited.