The books on magic and blessings both state that wizards and priests are at equilibrium when their power/favor equals their Willpower. The fluff also states that over time it gradually recharges/dissipates to achieve equilibrium.

So, I infer that wizards and priests start encounter mode with a number of power/favor equal to their Willpower. I justify this by saying that in story mode, these characters would just channel power or curry favor until above their Willpower and then vent until at their Willpower, and then recover stress and fatigue as required.

But, I can't find it stated anywhere that a wizard/priest begins an encounter with power/favor equal to his Willpower. I think it's implied, but it definietly warrants a direct statement.

Yep, that's how I read it. Just like the Stance meter, I don't see it state explicitly anywhere, but it is what makes sense. You start at equilibrium (ie WP).