It's all part of Apple's plan. They really want to take away those 2 GB from you, for no good reason. Kidding 🙂
Basically as several people in this thread have already pointed out, 64 GiB = 59.6 GB, where GiB is base 10, and GB is base 2 (See gibibyte and gigabyte on wikipedia). iPhone 4S firmware 5.0 weighs in at 797 MB, but this is compressed. Renaming the IPSW to .zip gives you the ability to extract the compressed files. In this case there are two files that contribute to most of the IPSW file size: 038-2711-006.dmg (794.9 MB) and 018-8012-343.dmg (17.1 MB). These are also compressed and unfortunately both of these are password protected and so it's not possible to determine the size of the uncompressed files in the .dmg files (the password is probably not publicly known). But either way, the OS partition is separate from the storage partition and so this does not contribute to the storage space reported in iTunes or About screen. Apple also doesn't completely fill up the OS partition. This is made clear when you jailbreak past devices and go into Cydia, then view the storage layout.
Hope this clears up some confusion.
tl;dr The storage size is accurate.