There are some good pictures in this thread about cliffys on ST:
http://pinside.com/pinball/forum/topic/stle-protected-cliffy-installed

I believe on ST just the rail itself clamps it in place. The hole is there for games where it interferes with a screw, like Metallica. Its not intended to be a mount, per se, just a clearance hole. The guide is on my Metallica page and linked from my ST (yes! Finally!) page http://www.passionforpinball.com/STStarTrek.htm

When I put it on my STLE, I put the lowest rail screw through the whole. It seemed to work fine.

Cliffy, I'm just tackling my install now. In your first picture,

http://www.passionforpinball.com/SternST/CliffySTLE-01.JPG

your arrow is pointing at the wrong plastic and the correct one is already removed.

From the other thread, here is the picture of the correct plastic:
http://forum-s3.pinside.com/201401/1413133/183145-i.jpg

That's how am seeing it, correct me if wrong.

I'm through that portion of the install. I used a combination of the process from cliffy's site, and that forum post. Wasn't too difficult. But can confirm, the plastic with the arrow on it on cliffys site, doesn't need to be removed to install the vuk protector.

However, it does need to be removed to install the pinbit protector for that plastic, so doing them at the same time is advisable.