I think that is one of the purposes of having the meta site. Instead of having long discussions in the comments of the question on the main site, it is neater to have the discussion here in meta instead.
I think if the suggestion is simple, we can leave a short comment on the question itself. If the issue is complicated, we should avoid cluttering the comments on the question and start a discussion either in Chat or here on meta.
The advantage of having a meta post is that it's contained in one place, but since the format of the meta site mirrors the main site, it suffers from the same problem - back and forth discussions are still messy, the important thing being that the mess is not on the main site. For the advantage of keeping the mess away from the main site in separate (labelled) containers, I suppose that such questions are on-topic here on meta.
Chat is excellent for back and forth discussions, but it's not contained in one place. A possible solution might be to create a chat room with the question owner to discuss issues.
(See: Users with 1000 reputation can create gallery chat rooms)
This allows the discussion to proceed more naturally than if it were in meta, and also allows it to be contained in one place.