Ah, I hadn't thought of that. Thats tougher to rationalize, but if I had to try I'd say lightning reflexes represents practice in dodging things that target reflex (area attacks, etc). Its not very good as there are some atypical abilities (Piercing strike comes to mind) targeting reflex, but its corner enough and not a huge difference so it doesn't bug my sensibilities as much.
Well, it's a game, you will always find examples that don't work well within the rationale... as long as it fits most cases, things are fine. The rest has to be put off as abstract, I guess.