Dave Bauer is your man for this one but I suspect that the folder_id is the correct answer because different revisions of an item could have different permissions.
You should be able to navigate the context_id tree using the permissions link from the site-map, and so find the folder_id object to set permissions on. I suspect that the link in file-storage just takes the pain out of finding the correct object to set.
We should probably decide how to tidy this up universally because I think that we are about to create a related problem in project manager if we are not careful.
R.
