This article is almost exactly the same as another article in Astronomy magazine about 3 years ago. I think that one was more complex then this article.
You can’t say that the Universe was cold, dark, and empty before the Big Bang. For that matter, you can’t really talk about anything being before the big bang, since there was no such time. Time and space themselves began in the Big Bang.
The large atoms which will eventually be the norm have nothing to do with the cosmic expansion. The thing is, there’s no fundamental limit nowadays on how big an atom can get, but if an atom gets big enough, then it gets very easy for the slightest disturbance to ionize it. The difference in the far future is that there won’t be any of those slight disturbances left.
The cosmological expansion just causes galaxies or galactic clusters to move away from each other. For objects of galactic size or smaller, internal forces are enough more significant than the expansion that they stay more or less the same size. In other words, the table expands, but the balls don’t.