In my view, the GTD methodology centers around the distinction between actions and non actions. We make action lists, we list someday/maybe actions, we flag actions by project, we list actions on calendars. Distinguishing the different types of actions and their contexts is extremely helpful.
However, GTD does not offer clear distinctions between the different types of reference materials other than to note that some reference material is closely tied to a projects ("support") and some is not ("general reference"). The main problem is that there are no clear distinctions between types of reference material. For instance, a single article may be relevant to several projects while also being a general reference item as well as part of a historical record for an earlier project or projects.
In short, in my view GTD is not the place to look for thoughts about reference filing (except for the point that physical items that are actionable should be treated and tracked as action items). I read the book to imply this when it points out that there are many different ways to file things. As long as a filing system preserves the distinction between actions and non actions, it complies with GTD.
For me, the most important design criteria in my filing system are: (1) Ease of use - especially for filing "general reference" items quickly. That's why I like Allen's idea about an A-Z system. (2) Physical separation - I separate phone books, textbooks, cheat sheets, project files, general files, archives, etc. so I can use my visual/physical memory to relate to the system (3) Ease of purging - I need to be able to gradually migrate closed projects out but be sure that I don't discard anything too soon (I work in the public sector and we must preserve records for set periods). (4) Conceptual separation - apart from general reference, I separate files along major topic lines.
I think the key with reference material is to recognize that filing is a separate issue from the action/non action issue that is at the heart of GTD. File based on what makes sense for ease of use, retrievability, purging, etc.