Wait, so I thought of another thing I'm confused about.
Spoiler:
In episode 2 Elizabeth goes back to Columbia, like I pointed out before. But besides the fact that Columbia shouldn't exist, it brings with it another thing that shouldn't exist. Comstock. If the events of the base game are still playing out, then that means that the Comstock from the base game is still kicking around stealing babies. So the Comstock from episode 1 isn't the last Comstock, or an anomalous Comstock. There is at least one more Comstock, and if THAT Comstock is perfectly fine, then there must still be millions of Comstocks unaffected by the ending. So what exactly did the ending even do? Did it even erase ONE Comstock?
Every place I've seen talk about the dlc's has never talked about these problems. I'm not so full of myself that I think I'm apparently the only person who see's these flaws, so I'm open to the idea that I must be the one in the wrong here. That being said, I'd still like these "problems" explained to me.