Gay marriage is accepted among wizards, and in the US it's commonplace for Muggle-born children to be taken from their families, who are Obliviated, and given to wizarding foster-families. Newt and Graves have been married a while before Graves got replaced by Grindlewald while Newt was in the field, and were discussing children. Modesty's whole family has imploded and she needs a new home. It seems only logical. It's rather more troubling under the circumstances, especially given Modesty's treatment with the Second Salemers and lingering distrust of magic.
Bonus points for:
- Alive!Credence panics when he hears Graves has her and launches a rescue mission, needing to have the switch explained to him.