I Just added a setting called:
suppress_reply_directly_above : Don't show in-reply-to on a post when there is a single reply directly above
The default is to suppress, however you can change it.
I enabled it locally and personally do not feel it introduces too much noise. I also avoid the expansion there cause it would be mega confusing, instead it just highlights the previous post.
What this did, form me, is highlight something completely different.
There are so many "direct" replies to the OP sprawled around the conversations that do seem to be making conversations confusing. I really do not see the need to make "reply to OP" in any way distinct to "reply to topic", it is just extra noise for no real reason, why do we need to make these two things different in the UI?