Freeman said she planned to take them to Earth to have them figure out how to keep everyone alive, but my guess is that inside, she was using this to pass the buck to someone else and privately was pessimistic about the chances of figuring out a way to separate them without Janewaying them. That feels like a very Freeman thought process. But yeah, they ought to have said something on screen.
The Bill thing at least is a joke about TNG season 1 - they had Troi call him Bill and it was in the early series bible that Picard would call him William and he would be called Bill by “close female friends.” I hate these shorts (although I’m glad they exist for the animation, at least), but that was a pretty funny callback.