I guess there is a conceptional problem with your idea. However it sounds interesting enough to think about.
Currently I managed to mod-in extreme world as starting planet. (Link)
In first tries, there was simply no production as it lacked production tiles, but my shipyard was operational from population number. Coming back to your idea, it seems you do need a hook for your shipyard, which in fact seems to necessarily has to be a planet. So far I couldn't see any other option, but I'm interested if there might be a way.
You may adopt and upgrade the idea of a dead world or...maybe a 'wormhole' from which your race may have originally came from. You will need a colony central, but you don't need any production tiles. Ok, the wormhole idea isn't much more then a planet with very different looks, but it may suit your planings enough to think about. Even an invisible planet is possible, while it still needs a colony center on it to link your shipyard to. Otherwise you won't be able to produce any ship.
If you convert your faction into a modded one, you may be able to back them with any ship you want. Just give them some station builders so you could equip your very first colony with a shipyard.