That's consistent with what I was saying. The ID of the thread you're replying to is part of the form data. When you reload, it keeps that. But the script used to enter and post comments without reloading the page in full doesn't know anything about that (it was likely made before such browser form saving was a thing), so it doesn't know to reposition the entry box based on the current data; and when you submit without starting a new reply, it just inserts it into the place it thinks it'll end up as a new comment.
Most sites don't use threaded comments anyway, so for them it'd just appear at the end as the latest comment - which matches how it'd actually look on such sites.
That's consistent with what I was saying. The ID of the thread you're replying to is part of the form data. When you reload, it keeps that. But the script used to enter and post comments without reloading the page in full doesn't know anything about that (it was likely made before such browser form saving was a thing), so it doesn't know to reposition the entry box based on the current data; and when you submit without starting a new reply, it just inserts it into the place it thinks it'll end up as a new comment.
Most sites don't use threaded comments anyway, so for them it'd just appear at the end as the latest comment - which matches how it'd actually look on such sites.