Most scientific articles are written as if the research followed some kind of waterfall model. In other words, a typical paper proceeds pretty linearly from the idea to the results to the implications of the research, hiding the fact that one thing might have lead to another in a very non-linear way.
I guess the reason for the linear format is to attempt to make the research easy to digest for others, and to keep the paper as short as possible. However, what should one do when following the standard format becomes a too large burden (e.g. excessive cross-referencing), or hides a key insight about the research process itself, which could be valuable for others to know?