Actually, that's not what chkdsk does at all. Chkdsk checks for errors on the hard drive - it has nothing to do with the OS, only the underlying hardware. It will search for cross-linked files, files with invalid names, etc., but it doesn't check the files against the "standard Windoze setup" at all.
That said, Chkdsk /f is one of my most-used commands for PC troubleshooting. It will solve all manner of problems that people experience with slow performance, boot problems, etc..
I won't split hairs here. If the utility finds errors with system files (which it checks for consistency) it will repair them. chkdsk /f will "fix errors on the disk." I've seen it bring a corrupt Windoze system file back in line and allow a boot. Chkdsk has evolved quite a bit from the DOS days, but I don't believe I necessarily misinformed in my explanation.