This is what I've read.
With Knox -- a rarely used Scottish/English/Irish surname and the middle name of Brad's grandfather, Hal Knox Hillhouse, the Jolie-Pitts established their own tradition -- instead of their sons bearing the same first initial, they share a final letter "x," and for their middle names, "n." And like Maddox, Knox is a strong name that has a good chance of being adopted by other parents.
Léon also has family connections, being the name of Angelina's great-great grandfather. It's also possible (though a stretch) that the name reflects his mother's charitable work, as one of the places she traveled to as Goodwill Ambassador to the UN was Sierra Leone.
Vivienne, the French form of Vivian, reflects her place of birth -- something her parents like to do -- and its meaning, "life, alive" resonates in the uplifting way that her brother Pax's name projects an image of peace. It wouldn't be too surprising to learn that this name was chosen to honor a family member or friend as well.
Marcheline is the French-sounding name of Angelina Jolie's late mother, with whom she was very close, and whose heritage was French-Canadian and Native American. An actress, she was born Marcia Lynne, which she seems to have transformed into a distinctive version of the French 'Marcelline.'
But it's all guessing as the haven't come out themselves and spoken about how they choose the names. Either way I like both of them...especially Vivienne it's such a throwback to another era.