Filing eMail doesn't make you more productive - really?

IBM research published an interesting study titled Am I wasting my time organizing email? A study of email refinding. It has been picked up in various places and looks like a field day for the "don't bother with organizing anything eMail" crowd. I think the paper is solid research for the question asked and the observations made.
However, I sense that a number of question haven't been asked that might change the producvtivity bottom line in favor of a different approach. I fully agree that hitting search or simply scrolling through a list of messages (often sorted by subject or sender) is a very efficient way to find a specific message. Also having a message thread is invaluable. I used message theads already in R7 when they only displayed when you open a message. So what did the study not look at (to be clear: I'm not saying they should have looked at these, but I'm saying you need to look at thse to gauge all over productivity):

• Impact on productivity of a full inbox. How much time do I loose to every time I look at the inbox to decide: that's a message I dealt with, this needs my attention?
• In Lotus Notes (other than Outlook) you can file a single message in as many folders as you like, so it is closer to tagging that "classical" folders. Once users know that, would they use it?
  E.g. I have a folder 1Action2Day and then customer folders. I move messages often into both. When I dealt with it I just remove it from 1Action2Day. Folders in Notes are equivalent to the tags in GMail, they could be a little more prominent in the mail UI (we do have the @Formula to show)
• In Notes I can at any time scroll and search in the "All Documents", so I don't need to settle for one or the other strategy. Depending on my needs different strategies work better.
• Difference in search strategy depending on short or long term tasks. E.g. I file "Thank you" eMails in a specific folder, so I can pull them out at review time. They are elusive to search since there are so many ways to say thank you (made my day, your'e the hero, awsome job etc). Also I use topic folders (e.g. a customer project) to review "what happened on the messaging wire". Using tags/folders I only need to make that association once when I process the message and not everytime when I search. So there's a huge difference between: "looking for a specific message" and "getting an overview what happened to {insert-filing-topic-here}"
• Knowing that search is available, does "remove from folder" shorten filing time (I use that quite a bit)?
• Impact of filing assistance tools. The paper mentioned one for Outlook and overlooked that we deliver one for Notes for a very long time: SwiftFile (unfortunately Windows only)
• Impact of ad-hock filing strategy. I didn't really create labels/folder upfront but create them as I go. I also do not file everything. But I do remove everything from the inbox

The interesting pointers at the end of the paper can be translated: classifying messages is boring (true), automated tools can/should help (true), more people information might help to (good topic for a follow on research). I would conclude: good meta data would be best (aka "What is the context of this message"), if it wouldn't be so unconvenient to create them.