It's not a big problem - just pick a reasonable instance, which 4/5 instances are anyways. Yes, if you pick an instance like lemmygrad on Lemmy that's specifically built to be an echo chamber, the chances of being defederated are higher. But picking a popular instance or an instance made for access to the fediverse (like what social.lol does) won't put you at much risk of being left out.
This seems like the correct approach. Two or three large instances with slightly different flavors that keep each other in check, then a long tail of specialized instances.