I think have this right. It seems as though mod skills are currently not adding any primary or secondary stats. At all. Halp!
Well, behold the power of chat: I brought it up when Nicholas was on IRC, and he claims to have fixed the issue. It should be in the patch that comes out today or tomorrow.
Sweet! I've been holding off on modding skills because of the rumors that this wasn't working. Didn't want to try to script and debug multiple skill trees if there was a chance the core abilities wouldn't be working.