Quoting Space Cadet Stimpy: All you can do is upgrade the ship they're fitted to
That is the crux of my problem, when I upgraded the ship the components were on, they disappeared. The new ship does not have them. They show up in the designer, I can design a new ship with them but I cannot build that ship in a shipyard or choose it as an upgrade version even for the ship that currently has the component. And yes, they are the same class.. I tried creating an upgraded ship with the parts but it does not show up in the upgrade choices, the upgraded ship shows as available in the designer but is shaded out in the shipyard menus and "You can only build one ship with component X" pops up. I deleted the original ship to see what would happen but no luck building the new one.
So, I am starting to believe that "only on one ship" may mean exactly that. That ship is it, now and forever. Better make it count because upgrades are not an option either. And if you try to upgrade the ship, the component is lost forever. Not sure if that was the intent or a bug or even just something weird with my version but right now choosing the planet based version during the ideological choice becomes the only real option unless I want to wait a long time since those precursor parts tend to show up on the first ten planets.