I agree, nesting is useful — but it would be great to be able to disable it by default in a core setting that impacts comment blocks. My experience is that most simple commenting is all aimed at the original post author, not the prior commenters, so nesting only confuses and complicates the interface. Nesting can be gas on a fire where there is a high volume of comments. Nesting can get out of control with noise and quarrels and buried good thoughts lost from the main thread. It needs more moderator attention. Substack is a good example of what can go wrong.
Some popular single author blogs do well with high-volume comments without nesting. A common etiquette is to @ refer to other commenters, which the post author might do in a single comment that engages select commenters. Ecosophia’s open thread posts are a good example of this. It’s not ideal, but it’s manageable for a popular single author blog where the author has to manage a regular comment flood.
Commenters replying to each other in public are probably the main source of trouble with comments, and making this easier for them is not necessarily a good thing. Do you want a micro forum where the replies to the OP can (or should) overshadow it? For Stack Overflow or Reddit, yes. For a historian’s or novelist’s blog, maybe not.