That's true, although as an individual that costs maybe ~$1k, and I imagine they get much better prices sending them a ship full at a time. I'd love to know exactly how much.
Plus intermediate parts (eg batteries) have to be shipped from China or the US until the factory itself is self sufficient, which may take a few years, and this eats in to the shipping savings. The Gigafactory Berlin plans currently approved do not yet include battery manufacturing.
As far as costs go, shipping is a distant third factor in the US/EU price difference (maybe 2%), compared to the import tariff (10%) and VAT (often >20%).
GF Berlin will probably be more efficient than Fremont. But so will Texas and whatever comes after.