Right now, I only allow specific races to build the default shipyard. I have added another shipyards with different prerequisites. Having the improvement as the prerequisite immediately deems that it has been met. Probably because it is colony specific or that the improvement simply exists within the ImprovementDefs.xml
I have tried having the improvement add a Stat or RaceTrait, but even setting those as prerequisites does not help . Too bad it can't give a specific free tech, then I would have an alternative.
Connected Github issue