The rules dictate that the time stops when the jingle finishes. Why not when the final hit is landed on the boss?
I have to admit, the asteroids can be a bit annoying, but they're far from random. They fly in the direction opposite to the side they are hit from, meaning you can hit one on the right side of it to make it fly left. It's not random at all, it's actually manipulatable.
I think that the rules for the categories (specifically "Beat the Game") are a little vague. Some clarification might be in order.
Fair enough, but the Nega Mother Wisp boss isn't really luck-based.
But you still need to complete the Nega Mother Wisp boss afterwards, which requires that you have all of the emeralds before facing off against the Nega Wisp Armor.
There should be a new category for the game where you have to collect all seven emeralds and face off against Nega Mother Wisp without having to complete all the missions or getting all red rings. Pretty much True End Any%, but I think "Super%" sounds better.