Developer of Baconit here:
As far as I understand from being a developer, the other section is used for apps and the app storage as you guys have suggested. However, when you delete an app the entire app and its files are deleted from the phone including all cache and settings files. What you are seeing is that even though the system removes all of the data, it cant reclaim all of the previously allocated room from the app as free space. I believe that the next time you install an app it will install into the space that was left from the old app and not add to other space unless the new app is larger than the old app.
That said, I think they only way to completely clear the other section is to factory reset your phone.
Again, this is just my understanding from what I have seen being a dev.