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For the kill team rules it says that the champion of chaos rule does not have any effect in the game, but if you purchase a gift of mutation would you be able to use the boon table then or is it just a waste of points?

Sounds like wasted points.

Chapion of Chaos lets you roll on the Boon Table.
Gift of mutaion lets you roll on the Boon Table.
One of those rules isn't used.
The Boon Table and Champion of Chaos are seperate things, barring one does not bar the other.

It's more than likely to stop a Daemon Prince rampaging through a kill-team, something that wont happen with a Gift anyway

I am thinking you can take it and use it still here's my reasoning you pay points for the gift of mutation and it allows a roll for the boon table chart before deployment and does not use the champion of chaos rule, you simply pay points to have a roll on the chart
I know of at least the dark eldar have a similar rule with combat drugs that allow you to roll on a chart before deployment.

Champion of Chaos special rule is just one way of Rolling on the Boons table. Other rules, such as purchasing a boon of mutation or utilizing the Tzeentch psychic power Gift of Mutation, allow you to roll on the Chaos Boons table.

I don't see a reason why you couldn't buy a gift of mutation.

Yeah, what the other guys said.

There are many paths to the favor of the Dark Gods.