Moved to the appropriate forum.
Aside from the question about whether such a change would be within the "spirit" of the GP system, I can tell you that it's not so much a bioware mechanic that causes what you experience, but instead the system we use to make subraces.
Essentially (and you may be aware), we apply "skins" which are something like magic items applied to a hidden item slot. This is how all subraces are created on Layo, and as such subraces are subject to all the bonuses and limitations that come with magical enhancements (such as not gaining extra skill points per level for a magically enhanced intelligence). You could consider this one of the drawbacks to balance the bonuses gained.
In other words, it's not a bug; the system is working how it's supposed to work. I play a tiefling who also gets a boost to his int via his subrace, and I also don't get the bonus skill points. Since it's not a bug, nor were you or your character subject to an unfair loss, a GP would not help you gain those extra skill points.