I think that the rules for the categories (specifically "Beat the Game") are a little vague. Some clarification might be in order.

What do you mean by clarification? You beat Nega Wisp Armor as fast as possible from a new save file. That's all there really is to it, other than basic speedrun rules that most games also do not directly state in their rulesets, such as no cheats, no impactful modding or no modding at all, no pausing the timer, cut the video to make sure that it is just the PB or close to it, watchable quality, no splicing, etc.

The rules dictate that the time stops when the jingle finishes. Why not when the final hit is landed on the boss?