Changing Disk Enumeration Order for Windows Setup

Having only a PCIe drive attached during install will accomplish the Disk 0 enumeration of that drive however, if the PCIe drive is attached to a secondary controller then you will end up with the situation I mentioned where the drive gets pushed up the number chain as SATA disks are added to the primary SATA controller after OS installation. To my knowledge there is nothing to prevent this and I would have to assume that depending on bios configurations you might experience this even with the primary PCIe controller. I have yet to see it but if I do I will not be surprised by it.

With the board I mentioned before having a secondary PCIe controller chip, this board also has two SATA controllers. In this case because of port mapping being enabled only on the primary SATA controller, once all primary SATA ports are in use the PCIe attached OS drive becomes next in line by disk number.

In the OP's first post it is mentioned that the PCIe attached disk is disk number 2. Board documentation will likely show that primary SATA controller port 2 is the first port where mapping is enabled. SATA ports would need to be enabled during install for Windows to see any disks attached that use port mapping. So even though not having SATA drives attached during install will enumerate a PCIe disk as disk number 0, mapping will remove SATA port 2 from being active and map 0 to that port.

So what you have here is that the primary SATA controller is the beginning of the disk numbering chain. Any PCIe attached disks will be mapped to occupy any SATA ports enabled for mapping. Once all primary SATA ports are filled/remapped then secondary SATA controller ports become next inline for disk numbers. Following that are externally attached disks so in most cases these days that means USB.