|I have to conclude this:|
The IDE card is completely usable in DOS without any other drivers. A CD/DVD TSR for DOS from the manufacturer's site is always recommended if you want to run DOS with your optical drive on the IDE controller enabled. (However, it may consume a bit more base memory, as SiI 0680 CD/DVD Driver consumed about 12K) I haven't tested whether other ATAPI drivers will remain work or not, but it's very unlikely.
Operating System installation discs should avoid using an optical drive attached to an IDE controller since they're unlikely to have built-in driver for the controllers, and they're unlikely to be loaded before leaving BIOS (where it's fully supported) and entering the operating system environment. A floppy disk or other media containing the driver of the controller must be provided in order to proceed.
Actually, it seems that all current Windows (XP/Vista/7 and x64 Editions), don't support these IDE controllers natively. Some other OS installation discs, like OSx86 discs, eComStation, will fail to boot.
I remembered that modern Linux can detect the IDE controllers without additional installation, but it may fail to mount the partitions from the hard drives attached to a controller...
Nearly all PCI IDE cards are not supported by the operating system itself, and they may or may not support ATAPI devices such as CD/DVD/ZIP and so on, and most PCI IDE chips are RAID-compatible, and only hard drives are supported by a RAID-compatible BIOS.
There's a risk when flashing BIOS: You should always use their official BIOS flasher (use other utilities like UniFlash may be risky), and always use it on a floppy, or on a hard drive attached onboard. Also, before you flash the BIOS, check your BIOS chip and find out if it can be reprogrammed since some are one-time programmable. You'll break the card if you flash it directly from a drive attached to the controller, or probably, if it's one-time programmable.