Are you saying that all captured alien races then become "generic" and all will exhibit the same characteristics?
No, they will be like your population with those exceptions mentioned. I know it's kind of a confusing statement, but your racial attributes and characteristics are a property of your empire, not of your population. The only real property population has is its atmosphere breathing, so that carries over. Your empire has an attribute that defines your native population as well. Any other populations in your empire will suffer the negative happiness trend.
Is that totally confusing or does it make sense?
Slick.I think it does. I'll try to put what you have said in another way.
Alien populations have their own characteristics when run by that alien empire.
Once conquered, all alien populations
1) retain their atmosphere breathing trait.
2) suffer a greater negative happiness trend.
3) take on all the other characteristics of the conquering race except for 1) and 2) above.
Would this be an accurate assessment? Or am I still missing something?
__________________
Know thyself.
Inscription at the Delphic Oracle.
Plutarch Morals
circa 650 B.C.
Alien populations (including your own) only have these traits:
Picture and Name
Atmosphere
All other traits are traits of the empire, not of the race itself. Other than the default anger increase/decrease, alien populations function identically to your own race's population because they do not have any traits save those mentioned above.