Note that the debossed dots don't appear to be punched. Obviously which slot a cover is put in doesn't matter, but I can imagine the obsessive-compulsive sorts are going to go bonkers trying to figure out which one goes where after they've been taken out. Also, there are too many dots to represent binary (101, 110, and 111 for example). The dots don't seem to correspond numerically to the braille equivalent of those numbers. The three I've removed from the machine are for slots 5, 6, and 7. I thought perhaps they were braille, but I haven't made sense of the patterns. I've tried to figure out what the dot patterns mean to no avail. Furthermore, the dots are on both sides of the tongue, with different patterns on each side!
The pattern of dots varies from slot cover to slot cover. If you look carefully at the PCIe slot covers of the Mac Pro 2019, you'll notice that on the tongue of the slot cover there are little dots debossed into them. Here's something I haven't seen mentioned before.