How can you make sure that commenters go equally hard on all speakers and their personal political sympathies do not affect their comments?
Yes, that can happen, though I think that the problem is made somewhat smaller by pointing out all fallacies, falsehoods, etc. That way, you can't cherry-pick fallacies and falsehoods that you want to focus on.
Another method would of course be to have several independent checkers, though that would be time-expensive. I had some people commenting on the comments draft, but the final decision was my own.