In my playthrough, I have commander choice and origins enabled. At the end of the soldier promotion process of choosing my starter abilities and choosing my specializations, a dialog (picture below) will display that my soldier has acquired a new starter ability. This ability is not seen anymore.
I'm guessing how RPGO works is that theres the diplayed userend, the function backend and the execution backend. When origins is enabled, theres probably code that disabled the execution but it forgot to also disable the function of the starter rolls and also the displaying of it. Thats why this false starter ability is doesn't execute?
https://imgur.com/a/2LBft0g