Looks like this confirms the accounting error. The backup files are only stored on your drive once, but count towards both Applications and iOS files.
I can confirm your confirmation sir! I went into an Apple Store in London earlier today to see if they could see me without a pre-appointment and they could. The 'Genius' who helped me had a very strong Spanish accent, y yo no hablo mucho Espaņol, so communication was tricky, but the long and the short of it was that he said the same as you, but needed to do a PRAM reset a couple of times to confirm the diagnosis and clear up the memory cache. He also said that it was probably an error by the developers that would be taken care of by the next update and that I shouldn't worry about it taking space. Hurrah!