To expand on this a little the two services make use of different well-defined objects in the AP standard. Lemmy communities are Groups in AP and top level posts are implemented as Pages (rather than Notes). As it stands Mastodon only has basic support for these two but a rework of Groups is listed on the roadmap as in-progress (https://joinmastodon.org/roadmap).

Do they really need to work that differently though? It seems to me that almost all of them can be represented as trees of text entries. Blog+comments, HN/reddit threads, Stackoverflow QAs, DMs, Discord/Slack, forums. These are all just text trees with optional attachments and/or links to other content (images and videos etc). Why not build that tree structure into the protocol (all you need is 1 parent and 0+ children for each entry)?

(Using Lemmy+Mastodon as an example)

Lemmy has the concept of "communities" - subreddits, basically. On Mastodon, you can follow a Lemmy user and see their posts+comments exactly as you'd expect. And you can follow a community too! To Mastodon's point of view, the community is a single user that "boosts" (re-tweets) every post and every comment made within. So following a moderately active community from Mastodon will absolutely flood your feed with 100% of the community's user activity.

Meanwhile, Lemmy doesn't do direct messages or use hashtags as a first-class feature. So if a Mastodon user tries to DM a Lemmy user, or a Lemmy user wants to follow a hashtag, they're out of luck.

And again, there are other Fediverse apps with even different models than these. Gitea, Forgejo, and GitLab are going to adapt ActivityPub to all federate with each other - this is a huge win, of course - but would we expect someone to make or review a pull request from their BookWyrm account?

They absolutely do not. This is more of a state of the ecosystem sort of problem. I think a lot of developers were wary of getting into how some of the more esoteric AP objects should work. It's important to note too that while we have a standard in the form of AP a lot of the decisions about norms for these less common message types simply have not been made, but we are definitely moving in that direction as more services add AP integration.