The hex editor part has nothing to do with the method itself. It's just explaining that the 00 (blank) values that the command line creates are more favorable for saving than the FF values that the R4 creates, I think.
BTW, that post is outdated, they updated it (By reposting) quite a few times, until they lowered the size of the file to 1MB (8mbit). The correct command is:
fsutil file createnew xxx.sav 1048576
(Where xxx is the name of the save file; It will create the file in the directory you are currently in)
Perhaps something that might be of use is the post by a user called "white," who seems to be analyzing how the game saves. It is pretty interesting, and the things he mentions may look familiar to anyone who has looked at the save file in a hex editor, and noticed the repeating headers. He posted his method in post 597, but it looks like he's still conducting his analysis (Judging by post 605).
http://game14.2ch.net/test/read.cgi/gameur...4256294/575-700