|There are at least two boot sectors on a hard disk and at least one on a floppy|
Every hard disk has a Master boot record. Each partition on the disk has a volume boot record. This is the same as the boot record you find on a floppy disk formatted to FAT12. It is this boot sector that is created by Format /s. Format usual gets the information to create this boot record from the system it is running on, that is MS-DOS.
If you have a floppy drive in your computer you can create a DOS Boot floppy within XP. There information to do that is stored in a DLL. The actually creates a floppy disk in Windows ME format which is based on MS-DOS the same as Windows 95/98
You are going to have to work out the details off how to do that yourself; it is a long time since I have used MS-DOS. What you are trying to do can be done, Windows XP does it with floppy disks, but it is not a trivial task,
Basically, Format /s is an MS-DOS command and has no relevance to Windows XP in the normal course of things. I would think of writing you own format command that will run under Windows XP.