Spent time thinking about it and there are still at least two universes at play in the story potentially.
First universe: The universe in which Belinda has roommates and was home at night.
Second universe: The universe in which Belinda's is Poppy's mom and works nights.
So, the way I think it works is this:
When Ruby defeated Conrad and the wish baby destroyed Conrad's wish universe, wish baby remade the universe into Ruby's understanding of what was happening (Poppy exists and Belinda is her mom, how UNIT functions, etc...). It's of course a little buggy but any wish universe would be.
They leave the baby with Ruby's family in the wish universe. Once back on the TARDIS, the TARDIS starts course correcting to go back to the first universe. This is why Poppy disappears and Belinda' goes back to who the audience knows Belinda to be relativ's backstory goes back to what the audience believes it to be. They're no longer under the influence of the wish baby.
However, Ruby remembers the wish universe because she influenced its creation. Since Ruby doesn't know what the audience knows, things get influenced in such a way that the Doctor forces the TARDIS into the second universe. Now, the second universe might be a fully realized version of the wish universe or it might be an adjacent universe that fits the criteria that Ruby would be looking for (Belinda's Poppy's mom, the wish baby lives with Ruby's family).
But we all know from the start of the series that Belinda goes home at night. She doesn't go home at seven in the morning. So the universe that the Doctor exists in right now is not the universe the original Belinda comes from.
Which then brings up some questions:
It's obvious that Ruby is the same Ruby throughout and somewhat obvious there must be two Belindas. Are there also two Doctors? Not because of bi-generation but just simply two universes in which a Doctor exists. I think the answer is no, because it seems like the Doctor who forced the timeline realignment (universe hopping) was probably always the Doctor from the first universe.
If there are two universes and Ruby is possibly in the wrong universe, then how does the Doctor figure this out and take Ruby home?
If there is only one Doctor, who is now in another universe from where we last left the Master, will we return to an Earth where the Master has been up to mischief or is he still a tooth? Although Fourteen and Donna are presumably in the first universe so they've probably got that sorted
It seems too repetitive though to break out of the second universe to get to the first universe because either a) the Doctor will have to regenerate again or b) we'll have to fill the TARDIS with companions again to get it back where it belongs. Or maybe this is how we finally get a multi-Doctor story instead of a cameo out of RTD [insert clown hat here]
Anyway, many thoughts head full. Not sure I would put any of this in a category of things I want to happen, but more of a category of things that could maybe happen.
I'll probably modify this when we get around to the end of the year special and get some more info and meet whatever new companion.