They can't 're-release' it, they couldn't even proclaim Xenosaga as a 'Prequel' to Xenogears, since Xenogears is a Square-Enix game, and the Xenosaga series is being produced my Namco...That's the reason it's all unclear.

Yes, the place under the Lighthouse was one of the best side-quests I've ever done myself. The main reason I go there, is for Big Joe's store... He has godlier stuff than that robot at the end of Deus.