Yeh, thought that was a bit odd, as this embedded utility is supposed to save a lot of preparatory work. Making a bootable floppy would otherwise involve messing about with a Windows 98 startup floppy.
Are you absolutely sure, though, that autoexec.bat and the Flash utility itself are required on the floppy? I appreciate that BIOS-flashing utilities have moved on somewhat over the past decade but when flashing a new BIOS on my current machine (by the traditional method of using a bootable floppy) it's highly advised to delete from the floppy disc, among other files, autoexec.bat. And, as I say, there's no mention in my user manual either of needing to put all three files on to the floppy, in the case of this new BIOS. It simply says "Extract the file and save the new BIOS file (eg. P55UD3L2.fl) to your floppy disk, USB flash drive, or hard drive". It then goes on to say "Restart the system. During the POST, press the End key to enter Q-Flash .....". It seems that, depending on the type of flashing involved, certain files other than the binary file itself being on the disc can sometimes cause the flashing to fail.
Could it be that the only reason why three files are obtained from the extraction, rather than just one, is that Gigabyte haven't as yet bothered to produce a zip file with just the binary in it? In other words, that the downloadable exe is an old legacy format?