What is actually the advantage of having two separate armours?
The biggest problem with the system is that mixed parties end up feeling non-optimal, with a single magic damage dealer feeling completely useless in a party with three physical ones.
That could be easily fixed by just giving all enemies one single armour value, which can be stripped away by both physical and magical damage.
The advantage is that it differentiates between enemies who are strong against physical and weak against magic, and the opposite, and it does this at a glance from the player. A single unified armor offers only elemental resistances as a difference between effectiveness, and you need to examine enemies to look that up. Don't underestimate the smoothness of gameplay resulting from being able to see what attacks would be most effective at a glance, instead of needing to carefully examine each enemy in an encounter.
You are correct about the problem with it, but it doesn't follow that going to a single-armor system is the only way to fix that problem. The main point of armor is to reduce the "swingingness" of CC effects. My tweak to the system of allowing all damage to pass through armor (while blocking status effects) does the same thing without merging the armors, and no math is needed.
If an enemy has 1000 physical armour and 500 magical armour, then they would have 500 new armour and 50% physical resistance on that armour.
Right now, resistances don't differentiate between armor and health. There isn't such a thing as physical resistance on the armor. That's just a flat 50% reduction in all physical damage, even once armor is gone.