Problem is each species handles environment differently, has (possibly) different manufacturing bonuses and infrastructure requirement
Good point - then the manufacturing bonus is the weighted average of all species in that population, the weight being the % of total population that species takes up.
As for environmental factors for habitability the game would have to track the infrastructure required for all species on that planet that actually require it and compute a maximum infrastructure requirement. Lets say:
500m humans who do not need infrastructure at all
100m of alien1 who has a colony cost of 1
50m of alien2 who has a colony cost of 3
So normally you need 15k infrastructure for alien2 and 10k for alien1. So for there to be no overcrowding this population needs 25k infrastructure. If there is overcrowding the unrest generated would be weighted based on the % of the population who are suffering from it so in the above example a 30% modifier since 30% is the alien population that needs infrastructure. In terms of deaths cause by overcrowding it would again be the weighted average of the affected species. So assuming a 10% death rate 6.67% of deaths would be from alien1 and the rest alien2.
The one thing I can't really solve is differing population densities - but that is tied to race not species.