You traced 164 pins and followed the circuits? Through a multilayer PCB ? I'm sorry, that is total BS.
I have repaired damage to MANY GPUs in last 7 years, the traces are barely visible, then vanish from top layer to connect through an intermediate layer and show up 3 inches away from start at a component on backside. And it is in fact the backside that you have pulled this claim from.
Without multilayer schematics and hours tracing circuits there is 100% NO WAY to make any such claim .
I call "shenanigans"
In past Apple changed just a couple pins on AGP connector for use with ADC display and people have had to tape pins 3 & 8 on cards for G4s ever since.
I suggest you recant, or admit it's option 1 or 2.
Or explain how your X-ray vision allows you to see the inner PCB layers from jpegs.
To be clear, I only looked at the general direction of where large groups of pins went and to what circuits they connected to. For example the first few pins go to a series of capacitors, which is consistent given that those are power pins, and the data pins travel to the processing core.
I didn't cross my mind that Apple would mess the PCIe 3.0 standard at all, but I will admit that we can't be 100% certain that everything is kosher just by seeing the back of the card, or even seeing the whole card if Apple messed with the pins before.
Does anyone know if Apple has ever messed with the PCIe standard?