hmmm....
I always design my ships within a setting so armor is just part of that setting.
But as a direct test I stole the Commonwealth STEADFAST-class Armored Cruiser (apologies to the designer) from the drydock sandbox and directly changed the armor into hull converted it to Commonwealth STEAD-OF-class Un Armored Cruiser ! The break points did change with Damaged now being one box fewer and Crippled more more, due I suspect to rounding. The CR remains the same and there is no difference in the game performance of the ship but you now have 1073 SU spare as apposed to 117 for the Steadfast. :? You can see the results in the sandbox.
Conclusion armor is pretty pointless in the game. :shock:
To easily 'fix' it my initial thought is to agree with RobinStirzaker to put the all the armor in the first undamaged section making an armored the ship more robust, by delaying the first check point, than a ship consisting solely hull. How to adjust the defensive rating I'm not sure. I leave the fancy maths to those with fancy calculators.
Another solution is to make armor some how different from hull within the game, such as 'Ignore armor' or 'armor only' with all that entails and I do understand the arguments against that approach.
A third option is to remove armor from the rules along side Carronades and Long-range Scanners.