That is a 'bug' (or feature) of any of the free ships designs.
If you obsolete the 'default' design you do not get the items.
I have seen the same issue with free drones for which ever trait it is that gives your the free drone, and expect it (though hante every had the Ideology trait) for the trait that gives your merchants free protection.
Short answer it dont' obsolete the 'default ships' or do so at your own risk.
(Now ideally developers, can we make the 'free ships' be built regardless of it the template was obsoleted)
