Perhaps that Alphabet originated on Gallifrey and the Doctor or some other Time Lord gave it to the humans?Then there's Cybertron where they use Greek/Latin based names... and also names based on concepts that wouldn't even exist on Cybertron, e.g. Bumblebee, Hound etc.
Maybe they represent numbers -- in Classical Greek Theta = 9, and Sigma = 200. <shrugs>