The stock file manager only shows a combined itemization of internal storage and SD card categories and how much each is taking up space. It does however show the exact same storage available for the internal storage.
I think what I'll do back up the entire phone and then do a factory reset to see if there is still a discrepancy. I'll be less paranoid if the discrepancy still exists. If it doesn't exist, then I'll be convinced that malware of some sort had made it's way to my phone and loaded on some secret stuff.
Would anyone happen to know whether I'd still be able to upgrade back to Nougat if I factory reset the phone back to its original state?