I would guess the original file structure was designed for hard drives, and was never changed. When storing on a hard drive, you want the data in a single file

I would guess the original file structure was designed for hard drives, and was never changed. When storing on a hard drive, you want the data in a single file to be located physically close together, which becomes more difficult if you're splitting up the file when you make metadata changes. Or, if the article's speculation is correct, Apple designed their formats assuming only 5kb of empty space would be allocated, which was insignificant even for the 1st Gen iPod's 5 GB hard drive. No reason to do more complicated stuff if a simple solution works. It only becomes a problem when people don't bother to keep track of how much empty space is being added automatically.