Maybe thinking about instances as “different things” is something that we just have to remove from our brains. Instead one could think of them more like “apps” (like RIF vs Apollo for reddit) since they all access the same platform...

Instances definitely are different things, they just happen to communicate with each other most of the time. I'm wary of too many analogies, but if you need one I think email is a better one than reddit apps.

• Like email, you have accounts with a provider (gmail/yahoo vs lemmy.world/lemmy.ml).
• Like email, accounts can generally communicate across providers (beehaw defederation shenanigans aside).
• Like email, you can't use an account from provider-a to log into the website for provider-b. You can't use your google account to log into yahoo.com, and you can't use your lemmy.world account to log into lemmy.ml. But as previously noted, you CAN communicate with users from that provider... you just log into your own provider to do it.
• Like email, different Lemmy providers might have slightly different rules for their users. Most of the time this doesn't matter, but sometimes it does. If you want to run a mailing list for 100k subscribers, you do that from mailgun and not a personal gmail account. If you want to run a sexysexsex community, you do it from an instance that allows that.

So that's a better metaphor, but mostly I think we need to move past metaphors and just learn what things are and what they do. When people taught your grandma how email worked, they used metaphors about the pony express, now people just know how email works. With federation, you're the grandma and people are using lousy metaphors to help get you started. But learn how it works and you'll be better off.