I am playing Terrans, and all my shipyards can build free ships if they are a cargo base hull design. Lots of Constructors and Colony ships!. These are all CUSTOM designs.
Also I find that using custom ship designs, I am overwhelmed by all the STOCK ship upgrades appearing for each and every technology researched. I don't see why "Soil Enhancement" should give me an upgrade to any ship let alone all the Stock ships!
This is annoying, but overall I am pleased with the gameplay.