Green races - I'm not completely against or completely for it, as I don't have enough experience with it. Maybe some practice green races with two players could be done as an experiment. It might be quite different in only a two player race compared to a fuller room. I've only done them in half full rooms ages ago but if I didn't get a boost it did feel like a massive let down sometimes. I felt quite reliant on it as my one way to have a chance. I don't think it's a less fair way to do it, as both competitors are exposed to the same level of chance, but I think in general people would feel it was less fair.
You could take separate polls on these things. But really you'd want a poll of the participants and not just a normal open poll.

As for the zone battle thing - you could just say that both players have to pick at least two different modes. That way no-one could pick three normal weapons on single races either. It might feel a little less like it was against zone battle that way, and guarantees at least a little variation in every match, which is probably a good idea if it's aimed at the best all around player, because they could otherwise get a route through the tournament where they only ever played weps on races, just by chance.