I tried to tackle this a while back. What I came up with was possibly being able to add an option to "repackage" the craft, trading it in for an inventory item which can be traded back for the actual craft. The inventory item would carry the same name and monetary value but would take up storage space instead of a hangar. You could then use it as an item in production.
You would just need to make some way to swap one craft for another. I was trying to use it for alloy interceptors--what I finally did was grant two options in the purchase menu: the actual interceptor, or a packaged interceptor. There was no way to swap between them except if you accidentally bought the packaged interceptor when you wanted the actual interceptor, you could sell the packaged one and get most of the money back.
That's the best I came up with.
