There is no (standard) BIOS call for obtaining the boot sequence, and as you say, DOS calls aren't relevant to Windows. However, it doesn't really matter in the case you're considering, because by convention only one hard drive (drive 0) is bootable.
Some BIOSes do allow you to select a particular hard drive as the boot drive. They do this by rearranging the drive order at boot time so that the selected drive is drive 0.
The warning message you describe was probably due to the size of the hard disk drive. Some older BIOSes can't boot to larger drives, and since the Windows installer had no way to tell whether your machine was one of the exceptions, it gave you the warning. (There are various other similar possibilities, such as the hard drive type.)
Assuming it did in fact boot, you don't really need to worry about it. :-)