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.