Instead of continuously manufacturing SOMETHING just to allow you to advance to the next turn, you should be allowed to let it idle if you want.
I see the new supply ships as a better option than idling. It would be different if we could see/adjust the ratio of shipyard vs. planetary production, but to my casual eye it looks like you'd be wasting production by idling a shipyard.
Then again, I haven't gotten into extensive playing with 4. I'm a massive-map, long-game player way back to the original Windows version. The current UI in 4 looks even more heavily designed to suit short, small games than the previous versions. The lack of a table-like view of colonies and another for open worlds slows me down immensely.
I'm also part of the crowd who want to be able to set rally points without having map focus pulled back to a shipyard. The current design assumes that the only thing you'd use a rally point for is collecting ships or dumping supplies on a colony. I've always also used them to 'make notes' on the map, e.g. marking pirate or space monster presence.