[President_Elect_Shang]

I believe that once you absorb those species into your empire they lose their native bonuses and take on your empires bonuses. As for their being differences yes. Kwok's Berserker's in the Balance Mod are a prime example. Now we are back to square one. How do you get those populations which are not absorbed and have a bonus to crew your ship so you can gain their benefit? You can't, as long as you control the ship it will have your species bonuses.