Viticulture EE is a very good, medium weight game that I've enjoyed at every player count I've played. It has a few things from the old version of the Tuscany expansion packed in, such as Mama & Papas cards (asymmetrical starting resources). So new Tuscany is a bit leaner than the old version, since they removed some stuff that I guess nobody liked.
Nothing in Tuscany EE will be in the base Viticulture EE game, so no overlap. The Moor Visitors expansion just fattens the two Visitor decks with some more cards. It is a nice throw in, but not at all essential. Those are also all unique.
Moor Visitors and Tuscany all fit inside the original box. The Tuscany board fills the box nicely, making it flush with the lid. I use small bags to separate the expansion player pieces, since I don't use them every game.
Board Game Geek has a file for cut out "meeple buckets", that you slip in the tray to pull out the player pieces very easily. Otherwise, it is a tight fit, and sort of annoying to get the player pieces out. Highly recommended.