Firstly, this is anything but a simple ship, with a level of detail that surpasses High Guard and approaches TNE.
Basically T5 is nit-picky enough that you must use software support, this ship is more-or-less defaulted by my Excel sheet, with minor manual adjustment. From my perspective, it's a very simple T5 ship.
OF COURSE your hull MUST protect against EVERYTHING. To not do so is SUICIDE. So the armor value remains, but forcing you to always choose the correct mix of anti-layers for BCS is Bad Design.
Agreed, just as in ACS, but here we are...
In other words, 4.8% for Jump-4, 0.8% for Maneuver-4, 1.1% for Power-4, all scaled.
Take my paragraph here with a grain of salt, because I like hand-crafting BCS. I admit to using software to build ACS; I don't like that either, but it's convenient and ACS is here. My critique is that at this level it's far too nit-picky. You saved 400 tons on a jump drive. Hooray! Except at this level, it's noise. Use the base system without stage effects, and pick by a table of percentages; it's not a different system, it's an efficient presentation that speeds the process along.
Stages have a large influence, e.g. indirectly through fuel volume, and that gives large differences by TL.
E.g. my ship would be 20% overtonnage without the drive stages:

Compared to with drive stages:

This is how TL differences are expressed in T5 ship design, if I step down to TL-14 I lose ~700 Dt, making the ship much less capable:

That is far from noise.
Again, what capital ship is NOT going to have FULL COVERAGE of ALL MEANINGFUL SENSORS at the BEST RESOLUTION IT CAN GET?
Those are very basic sensors, "the best" sensors would take thousands of tons, far out of reach for even most BCS.
In short, 5% volume to support the crew. Thom and I rounded up to 6%. Same difference.
Again, big grain of salt when reading this paragraph. Because you missed adequate defenses and tertiaries, your ship is likely to be gutted by secondary fire. But, you didn't actually miss defenses: you have an excellent armor rating. So perhaps "armor" also counts for the secondary weapon rating -- it should, right? So the design system has to account for that.
Armour protects against everything, except mesons.
A better classification for BCS weapons would be Meson, PA, Missiles, and noise, each with specific defences.
Meson: Screens only.
PA (whether spinal, bay, or barbette): Armour only.
Missiles: Armour, lasers, possibly dampers.
But that is exactly the problem with BCS. It's not ACS; it won't have the hit-location chart required for ACS combat. If it did, the combat system with squadrons vs squadrons would run longer than High Guard.
So BCS MUST USE ABSTRACT COMBAT, and what's more it MUST HAVE ABSTRACT SHIP DESIGNS. There's no reason it can't import ACS -- and to your point, it should, because isn't this T5?
But BCS is just another T5 sub-system?
BCS should describe the same underlying reality as ACS, just at a different level of abstraction. It should more-or-less yield the same results, just faster.
It sounds to me that you want LBB5 ship design, but with a higher level of abstraction in the combat system. But that wouldn't be T5 BCS, would it?