You are right in assuming the top level regs are generally missed out from any ad-hoc quest for information. Why would people go that high? It doesn't concern them and no authority quotes them.
In my opinion, the great majority of directors, managers and qualified staff don't refer to the top level docs, as Genghis suggests and, as Darkbarly suggests, the use of AMC and GM is well beyond most end-users' grasp.
I just wanted to add a comment. The top level reg is really the Basic Regulation and perhaps a few odds and ends. The 12 regs in my survey are the cover regs such as Air Ops or Continuing Airworthiness which are based on the Basic Reg.
For example, Air Ops regulation is only 4 pages, followed by Part-ORO, Part-CAT etc. While I can appreciate why one may not be interested in looking at the Basic Reg, I don't really understand why one would not look at the cover reg of those parts/annexes which apply to his/her work. In our example with Air Ops, the cover reg gives the intention of all the parts in Air Ops, so surely this could be of concern to the end-user. Also, the AMCs/GMs directly affect the end user in many cases and are intended to be one way of implementing the rules. Since the parts or annexes together with their AMCs/GMs are the lowest level of the regs, surely, that's the first place one would look?