There’s absolutely nothing wrong with a little centralization in your federation. It works well enough for email. The point is that you have the option, not that you have to use it.
You don’t have to trade one extreme for the other. In fact, I think this is the perfect example of that. Lemmy.ml is the developers’ instance, and by default would likely be the largest. Except… you know. Many, many people started there before going to other instances, especially the largest competitor.