You have seen this once already, but I place it here also for additional comment.
From your description, this would appear to be a noncompliance. However, there are other methods to consider. My quality manual references the specific procedure in the footer of the applicable section. For example, the section of my quality manual for ISO 9002, Section 4.2 references the specific procedure and the applicable section of ISO 9002 and the FDA QSR. BUT, that is not the only method. Do they have a document tree or equivalent? One facility I assessed did this. In the quality manual there was a reference in the preface to a document xxxxxxxx (i.e for additional information refer to…). There were no other references to procedures or anything else that might demonstrate compliance to 4.2.1. When I asked the management rep, he produced document xxxxxxxx, which was a detailed document tree, as referenced in the preface. From there, it was no longer an issue. The standard does not specify how the reference should be made, only that it will be. Since this facility is already certified, it would be my guess they may be using a similar methodology. But, it is only a guess.
As far as:
Each department will develop and document a system to define the processes…
I think that I might be looking for something more direct. I would make better reference to the documents, perhaps a line "Details of how we do this (achieve compliance) is detailed in our procedure(s) xxxxxxx". I agree with Don that Don's reference to an organization who achieved registration with vagueness in pointing towards support documentation should be carefully considered. Why take unnecessary chances, be direct and remove any doubt. ISO does not like the "gray zone". Good luck.