That's a good breakdown, thanks! The bad thing is that I could see these issues happening even unintentionally, with the fact that we have a few large instances vs. many smaller ones. So far we seem to have everyone running the same code, straight from the repositories (at least functionality wise). For my own kbin instance though, I have technically changed things. I changed some code to make a custom logo appear nicely, I've added some padding here and there, etc. I have also thought about implementing an automatic job that clears posts tagged with 'nsfw' or other related things in the microblog feed.
I might implement that, and then submit it to the kbin devs if it works well. There's no guarantee that other admins/devs would do that as well. If they implement a feature that makes their community more popular, they would seem to have incentive to keep it private. And that's where stuff like Meta comes in. If they implement rigorous content filtering, I doubt that would make it into the actual AP protocol. It would be the differentiating factor between using their 'safe' instance, vs. going rugged on an independent instance.
They could say "we implement the ActivityPub protocol as specified" and they wouldn't be wrong. They would just have some extras added onto the top to make their experience more polished. Easy to do when you are a for-profit and have plenty of devs. They would just argue that those are the features that make their interface different, like kbin and lemmy are different.
The only way around it is for communities to agree that they will run the software as released, maybe with only cosmetic changes. Any improvements to functionality should be submitted to the devs so that the wider community can benefit.
The problem is that if I want to communicate with Meta users, then my content gets copied onto Meta's servers, just because of how the fediverse works. Everything is a local copy first, then gets federated. So if I reply to someone who is a Meta user, in order for them to see my comment it must get copied to Meta servers. The only way to stop this is to defederate with them (which means the server you are on would not send anything to Meta servers).