In that case I strike my question and change it to: Why did whoever designed the troopers put those red dots there?
I dug through the "Art of Attack of the Clones" for you, Valin, and while my initial suspicions of Doug Chiang being responsible for the "streamlined" Clone look were more or less correct (he was the only artist listed as being responsible for the concept art of the Clones included in the book), it also says in the text that the final look was due to the sculptors and that the fin was added at the maquette stage by Lucas himself.
I didn't see any mention of the LED on the back of the fin as it applies to the film (it's one of those things you literally have to strain your eyes to look at on most televisions; as it is, I only remember it from the theatrical run of AOTC), but it seems like something that ILM would stick in there. But who knows; it could have been Lucas throwing it on there in one of his, "You know what would be cool?" moments that brought us Threepio's head on a Battle Droid and a farting Eopie.
I would think that this type of thing might
be mentioned in the Visual Dictionary for AOTC, but as I don't have that book, I can't check. Anyone else, as Valin's got me curious as to the LED's actual function now too.