I quite disagree. Of course interoperability is not going to be a perfect one to one - that's in the nature of these being different services. You don't want threads from a link aggregater taking over your microblogging feed.
Yet it's normal for Mastodon users to join in on the conversation here. From their perspective they never left Mastodon - from my perspective, I never left kbin - and you, for your part, think it's all happening within Lemmy. But it's really not. So these things happen all the time, it's just that you don't necessarily notice unless you check the domain of the person you're responding to. Mastodon users of course often leave in the @-tags, making them a bit easier to identify.
Lemmy is a bit more isolated than Kbin, as it is not integrating microblogs at all. That's a decision on the side of the developers, not a weakness of the ActivityPub protocol.