[Suicide Junkie]

Actually, I think ship armor is damaged from smallest to largest, and other components are typically damaged largest to smallest... but I think there's some randomness involved as well, because sometimes I see engines get destroyed before weapons...

Correct, although it is hitpoints that matter, not size. Most components have the same size as hitpoints, so this distiction only comes into play with mods and armor.

The B5 mod uses the fact that tougher internals are hit more often quite extensively. The B5 armor is simply high-hitpoint internals, so it gets hit more often, but is not guaranteed to be hit first.
Standard SE4 uses the "weaker armor gets hit first" feature for Stealth, Scattering and Emissive armor. The three above all have special abilities, and are much bigger, so they have more hitpoints. That makes the regular armor absorb a lot of the damage that would otherwise damage your extra ability armor