Also, I don't think aramid/UHMWPE make that bad neutron shields (compared to run of the mill PE, not magic Li-6). Boron carbide might be interesting radshield/CM material, combining radiation and ballistic protection, although I believe it might splinter.

In any case I typically don't rely on radshields for actualy radiation shielding for my non-stock stuff.
I prefer just shielding the reactors/NTRs down to around 20μW and having complete freedom of placing them around the vessel.

One of the points of using stock is to have absolutely 0 external dependencies.
I have been using aramid spall bulkheads for several versions already in my non-stock designs, although they are less effective with polygonal hulls.

In Garuda class I think a lot can be done with launcher placement, I don't remember if I already pushed my improvements or not.

In terms of armor, I like to add radiation shields composed of aramid fiber or UHMWPE in between modules in my ships. These don't provide any meaningful radiation protection, so their purpose is to stop fragments and fuel/ammo explosions from traveling around inside the ship, much like splinter protection in present-day warships. Maybe you can use those to isolate the launchers in the Garuda to help increase survivability? I don't know where you draw the line with using stock modules, but I thought I'd put it out there.

It's hard to say why it might be. Can be armour composition, geometry (further complicated by the fact that game's armour model is discrete and not WYSIWYG) or components in the harm's way (for example Garuda has some launchers that I have struggled to shield from enemy fire and sine those are stock launchers, they are full of explosive monoprop). Might be reduced coverage of csome layers to save on the mass (but that's probably not it as crew is protected and reactors highly redundant). I can bring my armour compositions to be more in line with Gryphon series (with bulk armour thickness modified apropriately)

This is the most resilient ship I've tested against so far, taking sustained fire from 1GW/m² lasers and more than 1000 9kJ Sandgun rounds per second for more than 2 minutes. and all using stock materials, this is marvellous. I wonder, however, why the Garuda class Dreadnaught can take so much less.