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1 - I don't remember models having a flag dummy :/. The Flag variable sets additional settings that have to deal with animations. This includes playing the animation backwards, or ensuring that it starts on frame 1 (since sometimes you can make it start on the frame it was playing from a previous state).
2 - Even though I don't have the model opened, I'm assume that EA created a double turret. One is for user control (e.g. turning and firing the turret) and one is just specific for transition animations (deploying and undeploying).
3 - Not sure what you mean
4 - AliasConditionState basically means "do the exact same stuff for this conditionstate as the one above me." It reduces the amount of repeatitive code needed for conditionstates that need to be the same.
DEPLOYED is a state when (like the nuke cannon) that the unit needs to be in to fire.
FIRING_A is the state when a unit is firing its primary weapon (In this case, the nuke cannon gun).