Step 1 is your problem.
Why do you have Arc open when modifying the settings? Of course arc will save to the xml (based on what is in Addin Manager) which would be nothing in this case, hence why your xml modification is gone. You need to give the settings PRIOR so the active session establishes those changes. I mention in my prior post...
"I would confirm in Addin Manager >> options that the folder path does indeed exist before closing."
meaning, under Customize >> Addin-Manager >> Options >> folders ... you would have noticed it would be empty. This is becuase Arc will ONLY read this xml file during Startup (initialization)
The settings must be established prior to opening a session.
Just like re-arranging your toolbars, buttons and customization, is saved on Shut down. (to the normal.mxt)... so empty add-in folder options (in the arc session) = will save the default xml string to the AddInFoldersList.xml. Arc does not look at that file DURING an open session, only on start up, and saves the information (contained in that arc session) on shutdown.
You could, open arc first, then modify the xml, open ANOTHER arc session, see the changes, close that one down, xml will keep the changes (as it saves them), then close the First Arc (which contains no folder settings), and your xml folder will be over-written with no folder path. (hope that is not confusing)
Hope that makes sense.
There is no bug, not sure why ESRI would say that.
Recap:
You should modify the xml as step 1. That is it!
Open Arc, you will see the folder in Addin Manager... when you close, it will re-write what you told Arc back to the xml as usual.
You should also, just ensure you are up to date with the Build 3200 level (service pack 2) and have the ten patches installed. (up to _34 in regkeys)