Really, don't delve into this type of stuff, you're going to drive yourself crazy. Here's an explanation though: Time Machine stores a local backup on your computer till you do an official backup. This backup never interferes with anything because OS X will automatically make room as needed. This backup is also hidden, which is the reason for the discrepancy. Keep in mind there are also a few other hidden folders that contain system files, so, like I said, it really is better to not delve into these types of things till you actually have issues. Macs tend to be very good at taking care of themselves.