On Lemmy, if nobody is subscribed to a community on your instance, it doesn't appear in that view.
In order for it to appear, someone with an account has to go to the search bar at the top right of the page and type in the URL to the community manually. Then it'll appear after an initial search.
On large instances like Lemmy.world, you can almost guarantee someone has already done this for most popular communities - but newer/smaller communities may not appear because nobody on your instance has searched for them yet.
For smaller instances, there are likely multiple communities missing and you'd have no idea until you went to look for them.
You have /r/gaming. /r/games. /r/truegaming. /r/videogames. /r/videogame. Etc.
Each community was slightly different in subtle ways, but some people were subscribed to multiple (basically identical) communities. Others self-sorted into different communities based on moderation style and community vibes.
Not to mention that your idea of how federation should work kind of ignores moderation and community preferences. Communities hosted on Beehaw are tightly moderated. There may be other communities that want something less strict. How do these two reconcile with one another? What happens if a conversation is removed on one instance but kept around on another?
If local mods only have local power, they can get quickly overwhelmed as you effectively need a mod team on every single instance. Smaller instances wouldn't necessarily have the manpower to have their own dedicated mods for literally everything.