I think that removing the Dragon Abilities feat altogether (to remove hardcoded bonuses) and replacing it with "fake" Dragon Abilities that will grant such bonuses as permanent buffs (in a more customizable way than the original) would be quite practical.
First of all, I could spread these bonuses gain however I wish and it'd look better to players (it's always more motivating to see bonuses rather than penalties, isn't it?).
Second of all, they wouldn't count as base ability scores, so they wouldn't provide an easy way to Devastating Critical.
Still, there are several potential issues.
First one I've noted is that dragon wings seem to be associated with Dragon Abilities feat. When I tried to use a "fake" one, no wings appeared during level-ups. Now, this by itself is of little concern, since one can add wings easily via some OnLevelUp script, but is it possible that this feat is associated also with some other stuff? Well, I have no idea what it could be, but it doesn't hurt to ask. If by removing this feat altogether I'm also removing something else from RDD, then this idea is very bad.
Another question: since these bonuses won't count as actual scores when determining feat availability, do you think there are any feats that could RDD should (and by should I don't mean they do in unmodified NWN) be able to get but won't be able to?
Finally, if that's the case I think I could simply, at a given RDD level, when I want ability scores to reach maximum anyway, remove bonuses from "fake" Dragon Abilities and give RDD a real one, which would then allow PCs to take any strength-based feat they previously couldn't.
Thoughts?