We’ve noticed this oddity too. I think the mental model our users have is that threads are by definition a chronological list of replies. Whether I’m replying to a new post or a post that’s months old, my reply goes at the end. Merging topics beaks that model since a portion of the thread gets inserted into the timeline at whatever point the moderator merges.
In the abstract, I can see the reasoning for the current behavior: it maintains the integrity of the conversation within the merged-in topic. But it also raises the question of why topics are merged in the first place.
In the case of our community, we want to consolidate discussion about a discrete topic in one thread. For instance, we want one topic for people to report whether or not they were admitted to Ohio State’s class of 2025. If someone starts a new thread, it’ll get merged into the official topic. The replies are often independent of other replies in the thread. Most of the time people use the “Reply” button to respond to a particular post, so it’s not quite so important that replies are close to each other on the page.
If the replies were tightly linked together, I’m not sure there would be a need to merge threads. Instead, it makes sense to reply in one thread with a link to the other. Or maybe both directions. And perhaps close one of the threads. Merging implies that the two topics overlap to a large degree. There are other (and better) tools for dealing with parallel conversations.
At any rate, I’m just adding a data point: this implementation of merging is difficult to fit into the mental model our users have and makes the feature somewhat less useful than it could be if the replies were ordered chronologically.