While I have not looked at the electrical layout for the board as far as controller positioning on the PCI-E bus yet I suspect that despite what the BIOS says (essentially software says) that WinPE is seeing the physical bus position of each controller.
The one showing first is higher (closer to position 0 iirc) than the other.
There may be no way to change this.
We run into this situation to some degree when we are setting up multiple RoC Hardware RAID controllers along side a number of SAS HBAs. Pecking order can become an issue.
Editing the ServiceGroupOrder reg key, adding an SCIS first entry, is visible in the online WinPE but it has no effect. The same can be said for changing the Tag REG_DWORD property of the iaStorA driver reg key. I used a valid value for the Tag value based on another driver which is also installed so as to avoid messing up by using an invalid Tag.
The site you linked kinda says, even though all this is true, it still may not work. So I don't know if it's a case of information being too old to be applicable, or there's some deeper interaction.
The only way I see of futher exploiting this technique is to actually edit the .ini file. I don't want to do this because I don't want to break Driver Signing. I think I have enough to go back to the stake holder and say, this isn't possible.
Thanks JFFulcrum, Philip and Edward for your assistance, even if it didn't get to the solution I hoped for, it was very much appreciated. It helped reinforce what I was finding independently. If anyone has any last tricks I'm all ears, but I think if nothing changes by Monday, I'll call this done.