What I don't understand what this has to do with focus firing, how the shield mitigation ramps up to high levels, etc. Can someone explain this in more detail?
Shield mitigation is an anti-focus firing measure. As ships take damage, their mitigation % increases until it hits a cap. This percentage is reduced from all incoming damage, regardless of the status of shields (a ship with collapsed shields still benefit from mitigation - in this sense the name is a bit misleading.)
if they bypass mitigation then they are always useful...
Yeah, phase missiles bypass mitigation.
Perhaps it's a math error, missiles do more damage to hull unless I'm mistaken, but with maxed phasing missiles my fleets drop enemy ships long before their shields drop,
You're right in a sense - when phase missiles bypass shields they also bypass damage mitigation, doing relatively more hull damage. This can probably result in ships dropping before their shields fail, especially against units with strong shields when compared to the hull.