Not sure about windows but the various Linux based OS's i've run have had no issue with the 5th SATA port in ACHI mode.
Were all running newer Bios though.
I did the install a while ago - in ACHI mode Windows wouldn't recognise a drive on the 5th port and the BIOS wouldn't install Windows / boot from this drive, only from Drive 1. May be different in RAID 0 - didn't try this, I only wanted drives in ACHI mode.