I think we do have to agree to disagree. Scaling Armor/AP by Mark is bad because it creates exponential damage scaling. For example:
Mark I Defender: 1000 Armor, 100000 health
Mark I Attacker: 1000 AP, 10000 damage
Scale Armor and AP by 125 per Mark after Mark I (so +500 at Mark V).
Defender
I II III IV V
I 10,000 8,889 8,000 7,273 6,667
II 20,000 20,000 17,778 16,000 14,545
III 30,000 30,000 30,000 26,667 24,000
IV 40,000 40,000 40,000 40,000 35,556
V 50,000 50,000 50,000 50,000 50,000
So Mark on Mark it is normally 10 hits to kill. Mark V vs Mark I is 2 hits, so the expected 5-times-as-powerful. But the reverse case of Mark I vs Mark V it takes 75 hits to kill instead of the expected 50. That is 50% more resistant to damage. In a straight up fight, the Armored Ship is much more dangerous to lower mark targets than high Mark Armor Piercing ships.
In case it isn't obvious, this particular case the problem mark scaling armor and AP has is AP does nothing once Armor is zero. But even if you take that out of it, looking at just the first row and you can see how the Armor scaling makes the Mark V ships 50% more powerful than their already x5 strength. Meanwhile, a ship type without Armor doesn't get that much more powerful at Mark V. This creates a discrepancy in how strong Mark V units are to weaker units.
Just chart it out if it still isn't clear. Even for small Armor scaling (+50 per mark), the above example is still a 20% increase in durability.