@shel Are you sure it's Mastodon's problem, not GNU social's problem? ;) As far as I know…
I think it's second. It used to not be visible on GS, because there were simply a few very populated instances. If you had your own single-user instance that GS behaviour could make you mad, because you were sometimes missing 70% of conversation, when people unknown to your instance (not followed by you) were replying to someone (followed by you) taking part in same conversation as you do. One of the main features listed on Mastodon's GitHub is actually a fix for that problem.

> Federated thread resolvingIf someone you follow replies to a user unknown to the server, the server fetches the full thread so you can view it without leaving the UI

Now, with 1000+ Mastodon instances, many of them somehow connected to GS, that problem (or feature, how some people call it) is just much more visible.