At a race as big as the Grands, the main should be the tie breaker no doubt, and in the case where the one rider didn’t make the main and still got #1 (at least in Jess’ hypothetical case), that really blows!
But, you are always going to have the dissenting opinion that “my son or daughter got a bad break and was wrecked by another rider, so it’s okay he got #1 with his points, even though he didn’t win or make the main.”
Take the point off the motos, put them on the main, and see what happens. Oh wait, the ABA already does this! Duh!