I might be misunderstanding OP here but that's not how I see it. In fact, the Mastodon web UI frequently shows profiles and posts from other servers on your own "home" server, in your own format. All example.org (your home) does is request JSON from eample.com (the remote), and displays it in whatever format fits your home server.
And it seems to me that it uses the first option that the author suggests, being example.org/user@example.com/thread
I can't interact with the sfba.social toot directly. Clicking 'boost' (retweet) gives me instructions:
> With an account on Mastodon, you can boost this post to share it with your own followers. Since Mastodon is decentralized, you can use your existing account hosted by another Mastodon server or compatible platform if you don't have an account on this one.
> On a different server
> Copy and paste this URL into the search field of your favourite Mastodon app or the web interface of your Mastodon server.
---
Similarly with 'reply'.
So, I can only interact with that toot on my home instance which is a bit of friction. Not necessarily a bad thing, but there's friction there.
Mastadon isn't too bad however. Interacting with it on my home instance only brings that toot over. One and done.
Subscribing to a community or trying to interact with a post in Lemmy, however, puts a larger and ongoing operational cost on the server as new comments appear and votes are cast.
That's when you start on example.org. But if I copy and paste a URL to you and you end up on the post on example.com, the best that Mastodon can do is suggest that you search for the link on your home instance.
And it seems to me that it uses the first option that the author suggests, being example.org/user@example.com/thread