Zexal is one of those things you can’t call plot holes for quite yet because they show a TON of foreshadowing and it’s far from over.
So it could be explained later. Actually probably will. You can’t say “this was never explained…” quite yet, because it’s not over and we can’t completely judge things like how many plot holes it has or character development quite yet.
Also I’d say that Yuma has subtle character development. he was a stubborn ass that never thought and he was a big embarrassing, but he meant well. Now he is still stubborn, but he /thinks/ and /listens/ to what other people (especially astral) say a lot more. He is slowly growing up.