Copy/paste from a comment I happened to have submitted a few minutes ago.
From a functionality perspective there is no difference. I'm registered to a Dutch server with this account and can comment on all OPs that are visible to me.
The administrator of a server (domain or instance) can block other servers (domains or instances) however. So if Meta not only starts it's own Twitter-like platform, but also it's own Reddit-like platform, it could be that administrators block access to the Meta server.
The best example for Mastodon (which uses the same federation protocol as Lemmy) is the Truth Social platform on which former president Trump publishes his posts. The administrators of Truth Social blocked access to all other servers on the fediverse, so Truth Social doesn't federate at all. And I presume administrators of many other servers block access to Truth Social.
So from that aspect, you might think through on what server you register. Might the administrator block access to certain servers? Do you want that or not? etc.
But you can also take location into consideration with regard to legal questions. I personally do not want to register on a server in certain countries if for example the GDPR is not enforceable.
Which, by the way, is also a great way to verify certain people. If a Lemmy account is registered on a server with a domain that is owned by a large broadcast company for example, it's easy to check whether the user of that account is who that person claims to be.
The municipality of Amsterdam set up their own Mastodon server registered to amsterdam.nl, so it's clear their Mastodon posts are genuinely from the municipality without any external verification schedule. If the mayor would want to post herself, she could simply get an account on that server and everybody knows it's genuinely her.
You also have to keep in mind that openly federating forces instance admins to, on some level, moderate the content from other instances too. Lemmy.world was forced to block some instances because it was proving too hard to moderate the content from them. You should also consider this when choosing an instance.
If an administrator thinks it's appropriate to block another instance, then who am I to complain if I use the instance free of charge except perhaps donations?
You're completely right there can be such reasons for administrators to block other instances and that's up to them.