Hey guys. I was directed to this post by a pm.
As to the questions in the first post. Those abilities that are referenced in the core race config but that are not in the faction editor, is because they are actually disabled in the AbilityBonuses.xml file and so if you chose them, then you wouldn't see any effect from the choice. Those abilities or any other ability you want to mod in could be added. Then you would just have to type the internal name of the ability in the custom faction editor and it would use it.
However, as you can imagine, I can't automatically come up with a value for custom abilities that is balanced against pre-made abilities. So yes, right now custom factions are not going to be balanced, unless you specifically try to make them balanced yourself.
As to why your changes to the CoreRaceConfigs.xml didn't work, you have to create a new file and save it in the mods directory (or race directory), you can't just modify the original file in place, it won't pick it up.