Personally, I don't see this as too much of an issue; these ships are slow and rare. While they eliminate the need for normal science labs in single player, they're still limited and wouldn't be able to easily satisfy all players in a co-op game. I think this adds to the benefits of grabbing one of these ships, and the recent addition of supply nerfs reduces their utility a little bit, anyway, since before you could take a few of these with a several thousand ship blob and research the galaxy, repairing the ARS as necessary. Because you're limited to nearby planets, they're more invicible now, but you still have a limited number of them and they're excruciatingly slow. If you want Mk II labs to be not so overshadowed, though, I suggest that their speed be increased substantially.