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It honestly wouldn't be that bad since the ending result is that both views are not opposed to one another, but rather they go together... IMO it would be similar to how they made ideals and truth both acceptable at the climax of BW...
It would be happenstance. You would progress through the region like you normally would but simply run into them and get tangled in their messes, and your player character by helping them out the first time would just bring an obligation every further time you bumped into them...
I would love if the team wasn't really evil. Note: this is not a BW tease where the intentions are sugar coated to look not evil with a leader that actually is corrupt.
I would love it if there were two teams that opposed one another, but their intention was not to be some over worldly goal...