The F6 key during the early phase of Windows XP installation is a way to tell the install program that you have hard drive drivers to provide for it, before it starts to look for hard drives to install on. It does not write to BIOS in any way, shape, or form.
I used to have an old Abit motherboard that actually had two serial ports (SATA) on the motherboard, but I still had to "F6" during Windows XP installation because XP did not know how to talk to the hardware SATA ports, and the drivers on the floppy diskette were the same SiI drivers you have. The interesting problem was that after hitting F6 Windows XP would ONLY look for drivers from the floppy drive, you could not provide them from an optical disk (probably the same for USB flash drives). That was Windows XP no-service-pack, perhaps service pack 3 had more drivers built into it.
SATA is backward compatible so I doubt the drive is incapable of booting from the PCI SATA I controller. I have found it very difficult to boot from PCI drive controllers. The job of BIOS is to locate a bootable drive and then to go to that drive to start loading the operating system. It seems like many times BIOS can't see PCI drive cards in order to locate a drive connected to them. They work fine once Windows is up and running, for instance if you are running a RAID array on it for data, but booting from them is another story.