Expandulated!
Our fluff for armor types is pretty broad. We use them to represent changing ECM environments, varying weapon loads, and the vagaries of active armor - a system we've intentionally left pretty opaque (see below.) In general, armor types (and now weapon, shockwave, and asteroid damage types, which just got added by Fury's request) can be used to handle elements of the battlespace that fall below the resolution of the FreeSpace simulation.
Active armor was originally just a conceit to justify rapid hull regeneration between missions, something akin to BattleTech's HarJel. As we looked through the FreeSpace fluff, though, we realized that even in the FreeSpace 1 era the setting had shielded missiles and other oft-overlooked peculiarities. Our armor fluff right now postulates that FreeSpace warships are studded with integral defensive systems akin to fighter shields, massive ECM abilities, banks of reactive armor panels, active countermeasures like laser pods, and a myriad of other defensive technologies.
If you played 'The Blade Itself', which it sounds like Thaeris hasn't since he apparently missed the reactive armor fluff there, you have an idea of how we'd justify improved resistance versus Maxims - additional reactive plating field-refitted onto ships, laser pods and improved targeting to degrade the ballistic characteristics of inbound Maxim rounds, fortified hull armor to tumble the munitions or otherwise defeat them, additional power to ECM or modifications to the software to degrade Maxim fire control (since we assume most FS2-era primaries use something akin to the FS1 Maxim), or applique plates to simply improve the thickness.
You'll also note that the Carthage was field-testing an armor system which improved resistance to Federation artillery and torpedoes, presumably operating on similar principles.
In general remember that these are ships that routinely survive dozens of nuclear-yield blasts. Postulating that armor of that magnitude can't be used to defeat kinetic penetrators is...odd.