This is absolutely not how reverse engineering a digital logic ASIC works.
Either the story got embellished through retellings, or this person was a fantasist.
There are people who hack on GPUs but it’s done at the software level.
I did get a kick out of imagining a scene where someone is trying to connect an oscilloscope to a circuit board to reverse engineer the CPU opcodes. That’s like the CSI: Miami version of what this would look like.
You'll have more luck reverse engineering the software driver first. They're not hidden, you can just open the driver files in Ghidra, the almost-universal tool for open-sourcing proprietary code. Hidden opcodes can be discovered first by just trying all the opcodes you couldn't discover any other way. You only need to go to the physical level if they're really hidden.
You can't tease out the right information by applying random inputs. Which input would you even use? The PCIe interface? You'd first "randomly" need to get past its complex training sequences...
Your postdoc probably wrote micro-benchmarks of some sort. That is a common technique.
So...agreed...far more likely there was a software solution of some kind if this happened.