Well, someone has to pack up their old apartment, and maybe they decided she should, so William can reconnect properly, maybe purely pragmatic. In the old version Miru had to leave towards the Ch6 I think, maybe that's Ocean's way for allowing Willi the space to cheat and develop relationships for the NTR aspect to start taking off?
Regards the changes, it might also be pragmatic - the story was too intertwined, this might allow a little more narative freedom without some of the massive complexities where every relationship hinges directly on every other one.
Well, I'm not saying I make 100% sense, just that there are all kinds of possibilities even from just what we currently know. I mean the basic premise that there are evil ganstas hiding in shadows throwing spiders into the Zane house isn't exactly the conclusion I would have reached, but here we are after that chapter
If Nika and Nami were put into custody to keep them from their past, that'd still follow the basic outlines of the SG story already, the big question is who are Willi and Leia's parents? That's really what I'm interested in, in both games, the MC has no knowledge of their past.