The "subset of the replies" issue likewise isn't inherent, but is somewhat more problematic as it requires everyone to behave in ways that makes it work, e.g. push replies back to the origin server, and regularly poll the origin for additional replies etc., and Mastodon itself is not great at his.
To the extent AcitivityPub itself is affecting any of it, it's only in the sense that ActivityPub imposes very few constraints on implementations, and that leaves a lot of room for specific applications to behave in counter-productive ways..