If you use “reply” on a given reply, you get a link back to that rather than just a reply to the whole thread, for example here
However if you reply to the last reply, rather than the “reply found at the bottom of the thread”, this link back is not present. As a result it can be unclear as to whom the reply relates. See this here.
Using the reply at the bottom of the thread, is like replying to the OT or the thread in general and not to a specific reply, but we can no longer tell the difference, if someone replies to the last reply.
This has caused confusion a few time of late and its seems to me a neish behaviour, but I am not sure. A work arounds is to assume the reply is to the one before, but we all know about making an “Ass out of U and ME”, or you can @mention someone, but most people do not.
(In general, blockquotes are a better, clearer, more flexible way of tying conversations together on a flat forum than reliance on single reply metadata. So if you want to have a policy, make it “blockquote all the things”. Remember the first toolbar button pulls in the full body of the reply in a quote if that’s what you want.)
As for in-reply-to suppression on immediate replies, we tried this both ways and it is very noisy when you don’t suppress the indicator in the following conditions:
when there is exactly 1 reply
when that reply is directly under the post it is replying to
Locality means a lot in conversations, and when one person stops talking and another starts talking, the vast, vast, vast majority of the time they are responding to what was just said.