Well the way it works in my head, phase missles are worse than a regular damage upgrade.
Heres my logic and calculations, could be wrong.
Lets say something(A) deals 10 damage. A fully upgraded (A) deals +30% more damage, thats 13 damage. Compare this to something (

that has 25% phase capabilities and the base of 10 damage.
So I'm going to assume the target is at full mitigation (60%) for these.
Against 60% mitigation, (A) does 7.8 damage when fully upgraded.
Against 60% mitigation, (

's missiles will phase 25% of the time, so 25% of the missiles will do the full 10 damage. So thats .25*10 = 2.5 , and the other 75% of the missiles will be doing regular, mitigated damage, and thats .75*10*.6 = 4.5 , add the 2 together and you get 7.0
(A) does 7.8 dmg/second and (

does 7.0 dmg/second. Even when the mitigation isn't 60% and it's lower, the benefit goes to (A), because bypassing mitigation at lower %'s gives you even less of a damage bonus over regular hits.
This is all assuming phase missiles can't bypass armor, but can bypass shield mitigation.