I think you are definitely right that there will wind up being some degree of centralization, even in the Fediverse, but I think the issue will be far less severe than the one we find ourselves in right now.

The fact of the matter is that it takes some degree of skill and willingness to devote time and resources to complete strangers in order to host a Lemmy instance, which will probably result in there only being a handful of "big" instances where the vast majority of communities are located. These instances could theoretically be bought, sold, and neglected, and potentially face the same conclusion as Reddit, bringing down whatever communities they happen to host.

However, the difference here is that some communities would be unaffected in that scenario. Suppose that Instance A were to go off the rails, taking with it for example the Lemmy equivalents of /r/gifs, /r/politics, and /r/gaming. This would suck, but at the same time other instances would be unaffected, meaning the Lemmy equivalents of like /r/news, /r/dankmemes, and /r/space could continue on. Furthermore, if the mods of those Instance A communities were aware of the possibility of the impending death of Instance A, they could form a migration plan ahead of time to another instance, and communicate this to the users ahead of time.

Compare that to where we are now, where literally every subreddit is shut down and needing to find an alternative place to land with practically no warning. I'd much prefer the federated scenario.