Mitigation works precisely how one would imagine - reduces incoming damage by that %. Despite the fact it says Shield Mitigation, it actually works at all times. Phase Missiles that ignore shields also ignore mitigation however. It also increases whenever the unit takes damage, and goes back down when not being attacked.
1 Armor = 5% Extended HP Roughly (i.e. a 200 health unit with 2 armor, will take 220 damage worth of attacks to kill, 3 armor would take 230, and so on), only applies on the hull. The advantage over just 5% health is that it's easier to heal/regen.