Substantive discussion is content which is about the subject matter of SO. It gives readers information that is independent of SO. If a change in SO would affect the relevance of a particular piece of content, then that content is not substantive.
Procedural discussion is about the relationship between content and SO itself. It teaches readers how to use SO. If a change in the world outside SO would affect the relevance of a piece of content, then that content is not procedural.
Similarly, substantive discussion on Meta is about SO, and procedural discussion on Meta is about Meta.
Examples of substantive content: code snippets, comments like "is that a typo?", and solutions to problems. Examples of procedural content: comments like "this is more appropriate for serverfault because you asked about load balancing in general instead of implementation in a specific language", "asking us to debug hundreds of lines of code isn't helpful for other readers", or "your answer is more of an advertisement than a recommendation based on what the asker actually asked."
When the two categories of content are combined, it looks messy. In active questions, it can be necessary to look through several comments to find procedural notes. It gets worse when someone replies to your procedural comment and there is substantive content in between your comment and the reply or when a comment on the original question and a comment on one of the answers relate to each other. Furthermore, when I'm reading a question that I didn't ask, I'm annoyed when I have to read procedural content that does nothing for the scope of knowledge that I intended to expand when I clicked on the question title.
I suggest a division between substantive and procedural content. Possible implementation: have a "normal mode" which is identical to the current interface, and a new mode that locks controls on the question itself, answers, and comments, and grays substantive content. In this mode, users can write procedural comments which appear in red and are hidden in "normal mode". They appear before all substantive comments on their respective questions/answers.