Getting USB 2.0 speeds strongly suggests that the cables somehow had horrendous signal integrity...

Anyway I grabbed a 3.1 gen2 SSD and plugged it directly into my 16" M1 Pro (Sandisk Extreme), and I got 850 MB/s read/write with his tool.

And that's supposedly one of the exact drives and laptops he tested. So something is going wrong for him, and it's 90% likely to be cables.

It doesn’t seem particularly likely to be the cables when the same cable plus same external drive but with an Intel Mac results in the expected performance numbers.

In your test, did you use a TB4 cable or a USB data cable?

Just because a marginal cable works on one machine doesn't mean it'll work on another.

I used a USB cable, but I retested with an active TB4 cable with the same results. And again with a passive TB3 cable to the same results.

If the cable is wrecking signal integrity, the port could absolutely change things if the ports have slightly different hardware that's generating the signal. RF does weird things.

Just as a very simplistic analog DC example, if you have wires that are both sitting at 3V but one can only drive 100 mA while the other can drive 1A. If you only draw 50 mA they'd look near identical but as soon as soon as you tried to get close to 100 mA they'd both diverge heavily. You could advertise both at 50 mA for sales purpose but if they were hooked up with a bad high resistance cable they'd look very different.

As a less technical anecdote, I bought one of those usb "sound cards" and it had noise when plugged into the front usb ports but worked fine into the back ones on the same PC.

The sound was transmitted digitally and didn't need that much bandwidth, so the only explanation is "dirty" power on the power wires, I think?