There is a workaround currently.
If you "check" the box to enable the Auto-complete design, it will update the transport ship to the latest design. It will also however create a bunch of design you might not want.
You can safely uncheck it after and delete the extra design. The transport will stay updated with the best tech that was available at the moment you check the box. If you ever need to update them again, re-check the box.
The bug is probably because you should be allowed to design the transport ship class in the ship designer, but you currently can't see it. AI empire will probably won't suffer from this bug since they probably use the auto-update feature by default.