The Reply tool makes it possible to reply to a previous comment. The reply (new comment) will be indented 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 row:
and another with a different structure (I think, this is what Flow/Structured Discussion uses):
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 indented, but there is another 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 solves some concerns raised here and in other tickets (for example in T249579, T249886).
T249579: [EPIC] Usability improvements: make the actions, activity and content within talk pages easier to understand
T249886: Create a new workflow for posting a comment w/o indentation
T264116: Reply inserted at wrong indentation level on ja.wp (after a comment with an empty paragraph)
T265750: Make it easy to "outdent" by changing the colons/list level