Reasonable upgrade, impossible to build a new one?

[shinigami]

If the resource costs in the rest of your mod are close to stock levels (high mins, low rads, extremely low orgs) one possible solution would be to add the shipyard ability to your capital facility but only give it the ability to build with organics. Then set the costs of your upgrades to a normal level except for organics. It is an ugly solution but it would work. The only real problem I can see with it is that if the mod also keeps a stock level of resource production you could easily wipeout all of your stockpiled organics and get the dreaded "Lack of Resources" message.

Does this make sense?

Edit: SJ's solution is much better than mine!