The firmware partition is not 200mb. The "200mb" that you see missing is from the fact that they define 1 gigabyte as 1000^3 bytes instead of the 1024^3 that your computer considers it.
The Apple firmware itself is ~5mb. On 5th generation iPods, there's a second 5mb for running the Broadcom chip. The firmware partition is between 40mb and 120mb depending on which model of iPod you have. This is to store the contents of RAM when it sleeps.