Most civilizations are of a single, specific species.  However, when you create a custom civilization, you can choose to have your citizens be of any and all species (which I did). The first screen snapshot shows this option.

The problem is that some of the Ideology trees have traits that are beneficial or damaging to "your" species or species other than "yours".  For example, the second screen snapshot shows the Prejudice trait within the Malevolence tree which says "Units that are not our species gain +2 Diligence".  What happens when OUR species is ALL species?

I believe this is an issue that you need to think through if you are going to allow custom civilizations to be any and all species and you are going to have traits that give species specific benefits or harms.