hatter,
Note that the Apple reference to fsck says, "If you're using Mac OS X 10.4 or later, you should use Disk Utility instead of fsck, whenever possible."
I think one reason for this is if you are having file system problems, you cannot completely trust any file on it, including the fsck executables. Thus, as the Apple article suggests, booting from the DVD (which is, of course, read only & therefore very difficult for it to contain corrupted files) should be the first line of defense, with fsck reserved for the situations the article mentions.
While it is true that Disk Utility (or the underlying fsck routine it calls) from versions older than 10.4.2 lack the ability to repair "overlapped extent allocation" problems, newer versions can't either -- they just supply info about what the affected files are, while older versions do not. This is "better," but not in the sense of a more complete repair.
Also note that a safe boot
runs fsck automatically, so it is not necessary to do both.