I think this could be part of the deployment system, whatever it will be.The industrial cost of making the ship will, hopefully, be independent of training the crew. Whatever system is used for actually manning and deploying the ship will hopefully have some kind of resource use.
I don't know if they are sticking with leadership, but it's a good touchstone for thinking about it. Imagine, once you've built the ship, you need to spend leadership to train the crew. The more training you give them the better the ship will perform, but the longer the training will take and the more leadership it will cost. You could even select different levels of training for different ship functions, and it would all get added up into the final leadership time/cost. If they don't use leadership, then whatever the training resource is would be the limiting factor.