We always get the uncapped mitigation value, subtract penetration, then apply the cap again. (example 1) If you have 47% crushing pen, and dummy has 50% crushing mitigation, you would be hitting it as if it had 3% crushing mitigation. OR
(example 2) If you have an uncapped 100% fire mitigation (cap is 75%) , get hit with a 20% fire pen, you now have an 80% fire mitigation but still capped at 75% since you are over capped.
Mitigation is always useful, and armor pen values were also toned down in 5.100.