SMT doesn’t portray things as they ought to be. It shows what they are. Would it be nice, yeah. Is it what it is, Nope. But if your looking for a nice version, Devil Survivor Overclock has it. That is, if you take any other route but Yuzu’s or Naoya/Kaido’s Route. If you want the best result, take Amane’s route. You’ll see what I mean.
But anyway, I feel that it is suppose to represent how religion portrays YHVH. Or at least, when you look at it from a non biased stance.