I'm pretty sure they intended for shipyards to reduce micromanagement by allowing us to build from multiple planets, so the fact that we are outproducing even at 1 planet per shipyard is a sure sign this isn't as they intended. This is just a killer problem right now as I have to micromanage my resources so that all the overflow goes into social. If I don't I lose all that production.
Speaking of which, lets have some overflow please. Overflow on research and production. I shouldn't have to waste my time preventing overflow loss on a modern strategy game.