Is it the only “artificial” specie you plan to add?
Maybe. This is basically a proof-of-concept that precedes serious though on what to do with them.
Multiple species are more likely if none of them are upgradeable.
It also seems your exobots can colonize asteroids and gas giants, and are able to have a significant population on those? Seems a little strange.
The gas giant thing was a mistake.
Are they generated as natives at the moment?
It should happen. I don't know how to prevent it. There's just one big list of species-- the only distinction on where they appear is if they are "playable" or not.
It should be easy to make an effect that gives a population based bonus to all your planets inhabited by Exobots.
If we made other population bonuses not effect them.
Also, I couldn’t build an exobot colony ship. The structure built and removed itself, but no ship appeared after that…
That's odd, it works for me. You should get a building, and on the next turn, it should destroy itself and give you a colony ship.