I don't know if it's still relevant, but I had the same problem and found a solution that works for me. THANKS!
After focusing on a project or folder, select "Library" and then save the perspective. Now the Inbox items shouldn't show up in the main outline view.
It seems kind of odd however, that selecting in the sidebar the actual folder I wish to focus on shows me the Inbox as well as the folder, and that I have select Library and save to the perspective to get rid of the inbox showing.
The second oddity here is that it has all the time been possible for me to not see the Inbox if I just select the same perspective a second time. If this is not intentional, I guess this is a good start for debugging.