The alignment is indeed a numeric value that goes from 0 to 99 (or maybe it is 100) where 0 is fully dark and 99 fully light.
The point changes for different replies are somewhat more complicated though. Basically there are three scripts for each side: k_act_darksml, k_act_darkmed, k_act_darkhigh and the same for light side. Which one of those is used is specified in the .dlg file. Each of these scripts then calls the UT_AdjustCharacterAlignment from k_inc_utility which calculates the actual value. That way you get more dark side points if you're light sided and vice versa.
If you want the exact calculations, check the k_act_darksml script etc. You can find those with Kotor Tool in BIFs -> scripts.bif -> Scripts, Source. The functions they call, can be found in k_inc_utility.nss which is also in the same path.
Just going to throw this out there for you Q if you want to make more than one skin (like alternates or whatever) for T3 and/or HK: with a little .uti editing and if needed 2da magic, you could make the skin change depending on what armor item/armor class the droid is wearing...
Sounds cool! I didn't know that was possible.
@others: No worries, you know how this turns out with my early previews
Here is a tutorial on how to do that, should you want to give it a try.