It doesn't affect the installation of the block or compromise the attachment.
Just was very strange to read. I believe the block does have a hole there for the screw but the gpu itself has no screw hole there. It would go through one of the chips (iirc) if you placed it where the instructions said. The previous step on the instructions even show there is no hole there.
You'll probably look at the 2 back screws and have a "***?" moment. They attach to the block in the corner of the fan cutout on the board. You have to use the included washers to spread the load.
Also it was very useful to use a tiny bit of thermal paste to stick the standoffs onto the block. They do suggest this but most people wouldn't do it.
I'll post some images in the build log (link in sig) tomorrow when I install the 2nd block. I'll show the screw hole which is unused if it is the same as the first one.
If you look in step 3, you can see the unused hole at the bottom left. In my copy of the instructions it says to put one there heh.
You'll also need to pull a bit on the heatsink to get it off once you've undone all the screws - that thermal paste they used has set pretty hard.
Also be careful to not strip the screw heads on when undoing them. Some of them have that threadlock glue stuff on the ends and are really tight.