What is the negative impact of using national troops (namely Indian, etc.) under command of the officer who don't have national troops usage skill??? Nothing listed in the manual.
The answer is, it depends. If the sub-faction is not a Native or Coop faction (i.e. GBT (British African) troops under GBR (Great Britian)) suffer a hefty CP malus. If they are Native or Coop, there is no penalty.