NPC's always included the racial bonuses. The problem with them in the past is that they also started with as many skill points as a PC, but the requirement that those points be spread out across the 5 skill groups did not apply to them, so a player was able to assign all their points to one group--say "General" and make uber-characters. Edited By: Gort Horth on Year 13 Day 14 3:45
The fix, was to remove many of those skill points so that they more resembled 1st-3rd level characters with far narrower training than points spread out across the 5 skill groups. That fix is a good one, except it was not accomplished for all of the NPC's in game. Someone apparently applied it to only a subset of NPC's, like the builders. Eventually, someone will get round to removing all those skill points from the older NPC's to make them more like the newer NPC's. We only have to hope they'll do it without screwing up the NPC builds. The only fair way I can see to do this is to remove all of the applied skill points and reset the characters as if they were new, then apply back all their XP and earned points. It would be interesting to know if this was done with the builders whom were apparently fixed.
Likewise, would be nice to have a flag that says which skills do/do not function with NPC's. If for example, we presume all NPC's in a squad share perception/sensors/scanning, and if the Perception skill works with NPC's, then it seems worthwhile to have trained Perception to level 5 in at least one member of most squads. That's a big investment and why most players don't assign the free skill points to NPC's yet, because we just don't know what will be enacted when or how.
My psychiatrist told me I was crazy and I said I want a second opinion. He said okay, you're ugly too.