WAIT WAIT WAIT
I got it. It makes perfect sense.
Each spell is on a different input. So, let's say that Thunder is Neutral, Fire is side, Wind is Down (which makes sense because Elwind is pointing down). My theory still sorta applies but it's not all mapped to Neutral B. Basically, let's say that you cast Neutral Thunder twice. Like I said previously, it starts from the weakest tome, Thunder, and works it's way up, to say, Arcthunder. However, afterwards, you use Fire. It starts at Fire and not Bolganone. And you use it again to use Elfire. The tomes all cycle, but they're all tracked separately on each Special input. So you can have Arcthunder loaded up on Neutral and still have Wind and not Arcwind on Down-B. This is perfectly consistent with female Robin's part, too. She uses Arcfire, then moves into Arcthunder, and uses thunder again, which is Thoron. Once each tome has reached its' most powerful version, it resets with a cooldown.
Am I making sense?