Why are you still on 10.12.1, macOS Sierra is now at 10.12.6 you can download and them install this, Download macOS Sierra 10.12.6 Combo Update once you have done that then check the App Store for any other updates you may want to install.
This may help with your Storage report in About This Mac.
Have you ever tried to re-index Spotlight, this can often sort the problem of incorrect System storage count.
System Preferences> Spotlight> Privacy click the + button and add your Macintosh HD to the list.
Now highlight the Macintosh HD and click the - button to remove it.
This should force Spotlight to re-index, give it time depending on how much storage you have on your disk or other disks attached to your mac.
to check whether Spotlight is re-indexing type something into the Spotlight field (the name of a file or folder you that exists) the Spotlight window should expand and you should see the text Indexing with a progress bar which will fill in blue as it progresses.