From my new-and-limited understanding, it can potentially be an issue if similarly- or identically-named instances are on different servers - someone over on Lemmy noted that the mod of lgbt is also the mod of conservative. If you don't know a post is from X@kbin or X@lemmy that could be a source of confusion depending on the quality of the different source-communities.
In the grand scheme of things, presumably whichever one is the more user-friendly will get the audience share and the other would wither away to the footnotes of history, but it's still a potential issue in the meantime. Happy to be corrected if I'm mistaken on all this, still very much a beginner here.