Part of the drive's total capacity is used for the data structures that keep track of all the files. There's always a certain amount of overhead involved with any storage media, and that overhead is larger the larger the drive is.
This has nothing to do with base 10 numbers. The difference between 500 GB where 1 GB = 1000x1000 bytes (the current measurement) and 500 GB where 1 GB = 1024x1024 bytes is much more substantial, and does not represent a difference between total capacity and total useable capacity.
Not sure what your point is, but "disk size", "total capacity" and/or "available space" (depending on where you are looking at the info) have always varied directly because of both the binary conversion, and the sector size.