The [[ https://www.mediawiki.org/wiki/Talk_pages_project/Beta_Features | Reply tool ]] make it possible to reply to a previous comment. The reply (new comment) will be intended compared to the previous comment. If someone replies to an earlier comment, it goes at the end of the of the reply chain.
This behavior is against the guidelines and the common practice on some projects, and it is not practical on extensively used discussion pages, like village pumps, RfC pages etc.
For demonstration purpose, I created a page with 70 replies in a raw:
* https://hu.wikipedia.org/wiki/Szerkeszt%C5%91vita:Samat/current_structure
and an other with an other structure (I think, this is what Flow/Structured Discussion uses):
* https://hu.wikipedia.org/wiki/Szerkeszt%C5%91vita:Samat/proposed_structure
The latter is much more dense/compact, the replies arrived later stay together with the posts they replied on.
There is a third option, which might be the best solution: if someone reply on a post, their comment is intended, but there is an other link which makes it possible to add a comment to the section (and not a direct reply on the last post) without indentation at all. This needs smaller change on the current behavior, but solve some concerns raised here and in other tickets (for example in https://phabricator.wikimedia.org/T249579, https://phabricator.wikimedia.org/T249886).