OK, after one long night I think I know at least where the problem is:
- QPI and MRC driver (most likely)
- SB driver (maybe)
The first driver's responsibility is so-called "QPI and Memory Reference Code". OEMs use the reference source code provided by Intel and then subsequently change it to fit their motherboard design. The second one is, I suppose, related to the southbridge.
Why I suspect that it is the QPIandMrc driver? Well, this is the code where you implement various errata handling strategies related to the various silicon steppings. It could very well be that ASUS just removed older code paths handling specific behaviors of A1/B0/B1 silicon.
Thing is - you cannot just swap this driver from a board that works... If you try to do it, you will immediately be hit with 55 error during boot (CPU cannot see the memory), which suggests that this code is most likely customized to the specific board layout.
Funny thing is, swapping QpiAndMrc from Z9PE-D16 will work, but you will not solve the 5A issue. Swapping QpiAndMrc from P9X79 Pro or Supermicro x9dai will end up with error #55.
Another interesting thing I noticed when looking into those EFI drivers - it appears Supermicro QpiAndMrc driver is almost the same as Intel's W2600CR, including the debug symbols that are still in. ASUS drivers are much smaller in size, and do not have debug symbols. I suppose ASUS changed/extended this code heavily as they allow memory voltage tweaking unlike Intel or Supermicro.
So, all in all... this means that the only way ES1/ES2 silicon could work is that ASUS fixes this issue, or leaks some older BIOS image. Unfortunately I do not have the tooling necessary to debug this as this would require at least AMI DebugRx dongle and probably also JTAG connection to the board itself.
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