I don't know much about PLX other than it being related to intelligent switching. I assume they are talking about the two "Switch ASM 1480" chips sitting between CPU1 and the first 4 slots. I'm seeing that in the "Z9PE-D8 WS block diagram" found in the manual... but it's still connected to CPU1, and logically a CPU seating issue would still apply. Unfortunately the manual leaves much to be desired in clarity and there's not much help for troubleshooting.
It sounds like you had a more fruitful discussion with ASUS than I ever have tho... Awesome! Maybe it's because you offered up the warpage possibility first. Each call for me was mostly met with an offer to RMA for a replacement, and when I told them the Q-code that it stopped on (not listed in the manual's list), I was simply told that it's a hardware problem. Sounds familiar.
It is a very complex motherboard and PCIe seems to be very sensitive. I even had difficulties just getting it to post at first. I haven't been able to get their PCIe wireless card to work... (either my original purchase or a replacement).
Sometimes you have to strip it down to minimum config with 1 stick of RAM in DIMM_A1 or 2 sticks (A1 & B1), and a single PCIe card (GPU), and clear the CMOS RTC RAM, to rule out RAM anomalies or weirdness in other cards. Then try the GPU in different slots.
It's really about experimentation...
and RMA is a long process if you choose to go there.
You'll get it eventually.
If Mom is too slow repairing the hole in your jeans then, "sverte ræva og gå naken"