At the last moment Newt realises there's a legal loophole which can save Jacob's memories: intermarriage may be illegal in NY but they have no jurisdiction to prevent engaged or married mixed couples with a legal address in another country from keeping their memories.

So Newt abruptly declares that Queenie hasn't had the chance to hand in her resignation yet but that she's totally taken up a live-in secretarial/editing job at his place in England and since that makes Queenie a "foriegn" witch engaged to a No-Maj it would actually be illegal by international magical law to take Jacob's memories. Which is how Newt managed to ask his girlfriend's sister to live with him and proposed for his best friend before admitting any feelings for the woman he loved. Awkward.

Bonus 1: Picquery knows he's full of sh*t but let's him get away with it.
Bonus 2: When the ehm, Fantastic Four get on the boat to sail to the UK, they find Credence and Modesty hiding on board.
Bonus 3: Kowalski's Bakery does happen, but with one storefront on a muggle street and the storefront at the other end of the building in Diagon Alley. Queenie and Jacob (and Credence?) just ahve to be careful not to let any of the enchanted pastries sneak through to the muggle side of the sho.