NWN doesn't have a system for stacking; its various spell and item scripts arbitrarily check for the presence of other effects and occasionally suppress them from stacking. That's the opposite of systemic. It's arbitrary and was vulnerable to (a great deal of) human error.
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Arbitrary meaning it was up to individual scripters to check for effects across the various ones used in the game. Effect types and stacking rules were not explicitly built into how the effects worked. It's very easy for someone to add a new script applying an effect that modifies a stat and never checks (or is never checked for) other effect states on the character. To be honest, I think it's pretty weird that you like how NWN's stacking rules work. Considering that stacking rules were almost universally seen as a positive thing for D&D, and that NWN's ability scores (especially) got incredibly out of control because there were virtually no stacking elements in place for many things, it's an odd thing to support.
When we brought the stacking rules to the attention of WotC during NWN2's development, they were very much in favor of switching to an implicit no-stack system instead of continuing with NWN's method of implicitly stacking most things.
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The IE built effects through item properties in the item editor or spell effects in the Spell-O-Matic. In IWD2, bonus types were built into the effect parameters, with types pulled from code and resolved in code (including "unnamed"). Stacking logic was resolved at the code level; it was not dealt with in the parameters or logic of a script, as it does in NWScript. Some armor bonus types are built into the NWN code base, but most of the other effect types are not defined anywhere. Of specific merit, enhancement bonuses essentially don't exist. That's why you can easily get dudes running around with 50 Strength: most bonuses are of the same undefined type, so there's no way to sort them. If applied bonuses in NWN had an bonus type parameter built into them 1) they could have been sorted according to THE RULEZ and 2) builders could still have applied bonuses with the "unnamed" bonus types to produce monstrous 50 Strength 10th level barbarians for their own campaigns.