I don't know enough/anything about ActivityPub, but maybe different...apps? (Mastodon et al vs kbin/lemmy) could have different agreed-on rules. The forum-style ones would be appropriate in search results, so they could be indexed. People linking to Mastodon posts on lemmy might be unavoidable I guess, but there's at least a bit more separation.
One thing i do hope though is that if instances that want to hide content, or users hide content, that the instance also publishes that data during syncing. Which is to say, i want to write a custom instance but i don't want to mistakenly leak something someone wanted to be private.
In theory it's a well understood problem-space in the Mastodon stack, so hopefully they only federate/publish what they are okay with being public. But it's concerning regardless.