"Each "copy" was a unique document in that they had all been circulated for review and comment and each had it's own collection of comments attached."
Do we know this as fact ?
A "copy" with a handwriten note or a postit would be an original of the note or postit, it appears to me...
I could imagine security being lax if all he had access to were copies of everything, he had clearance to read them anyway and distributing them would be against other laws.
I can't see any reason for anyone to be allowed access to any originals - I would be very interested for some insight by someone who truely knows the procedures.
I don't have first hand knowledge of this but have heard fom someone who knows what happens to these documents and how they are handled.
Each copy of each revision of the draft circulated to different locations (Say, one to the White House, one to the Pentagon, and one to Justice) Each copy then collected a different set of comments and found it's way back to the author (Clarke in this case) The copies, once dealt with by Clarke are then Archived with their comments.
I think your assertion that further copies are made in the Archives is misguided. When you are guarding secrets why would you unnecessarily double your task by making copies?
Surely, the fact that they are originals is why the eloborate procedures for handling and guarding them are in place.
If Berger was placing stuff in his socks it is hadly likely he would get 8 x 11 pages in there, but post-its are a distinct possibility.
I still believe he was sanitizing the comments, thats why he wanted all the circulated copies of the drafts.