I have the original release of Leander. There are no holes in the disks. The code on the disk doesn't write anything besides hiscores. There is a protection routine exactly where he says there is, however what it does is check for a long track. It waits for the index pin, reads lots of data from the track, then looks to find two sync marks in the data it read, and they're at least a certain distance away from each other. No lasers, no holes, no writing. Standard long track protection. Here's the whole routine: https://pastebin.com/c1wnaJBP
If you watch the original video, the person OP is talking about referred to an arbitrary hole that they added themselves/the disk producers added. The index hole is a normal feature of floppy disks that are "flippy" (usable on both sides).
In addition, OP wasn't talking about the index hole, which was only used on a few platforms. They're referring to the index PIN, which is one of the signal wires that comes out of the floppy device.
The index pin gives you information on what sector is currently under the head, but after reading the code OP posted and the Amiga documentation, you're correct that this was specifically referencing the index hole in the CIA's flags. So my apologies, you were correct and I'm eating crow.
I have the original release of Leander. There are no holes in the disks. The code on the disk doesn't write anything besides hiscores. There is a protection routine exactly where he says there is, however what it does is check for a long track. It waits for the index pin, reads lots of data from the track, then looks to find two sync marks in the data it read, and they're at least a certain distance away from each other. No lasers, no holes, no writing. Standard long track protection. Here's the whole routine: https://pastebin.com/c1wnaJBP
Here's a page that more accurately describes floppy disk protection methods (and also explains what a long track is): https://diskpreservation.com/dp.php?pg=protection