[CUnknown]

Let's say the one evil top dog will win even if his secret enemy is not defeated. The main evil force can probably make his secret enemy a slave vassal anyway.

And also remember that you don't have to actually destroy your secret enemy, only ensure that his/her capital is captured (by anyone, not necessarily you) or that their god is dead at the time of the Ascension. Slightly easier conditions for Evil than complete destruction of the secret enemy.

Edit: One more thing, if the Neutral races are getting iron mines in their capitals, does that mean that their starting positions need to be fixed beforehand as well?

Do the Neutrals need iron mines? We are playing at +25% resources, after all. I'd rather the Neutral starting provinces be random. The Neutrals will get 1500 gold and 10 gems of every type to start.