I've figured out how you can get alien civilizations to not have the same number of ethics/traits that you do. In order to get everything positive in the base game for traits/ethics you need the following:
32 Trait Points
16 Trait Picks
8 Ethics Points
After you get that while editing a race, select done. This brings you into the screen for determining galaxy size, number of alien civilizations, etc. Go back into the trainer and edit the numbers above back to their default values:
3 Trait Points
4 Trait Picks
3 Ethics Points
Doing this will allow you to keep your cheated numbers while alien civilizations are stuck at the defaults to work with.
Hope this helps!
The issue however is you would have to do this every single time you start a game, you can't save the race you customize with this trainer, it would automatically disappear.
The way I did this was I created a custom race and used the trainer to get 99 ethics and traits ect and picked whatever I wanted. after customizing the race to my hearts content I saved the race and then restarted the game without using the trainer and just hit new game and had no problems. I used observe command to make sure every race only had a few traits ect and have had no problem otherwise. I haven't played this since the game released however so I'm not sure if anything has changed in the game currently with the new patches so I apologize if this is no longer a valid method.
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