Looking at it realistically two species, developed in different solar systems, with entirely different biologies, would be incredibly unlikely to be able to produce viable offspring, assuming they can even get their genitals (them having genitalia at all being another assumption) to fit together at all. Regardless of their similar appearance (which is what a phenotype is, outward appearance). Even on Earth only incredibly closely related species can produce offspring together. From a gameplay perspective such a feature seems pretty minor, disproportionately difficult to implement and a little bit ridiculous. I wouldn't be too happy if it was in the game, and I do not expect it to be at all. Interspecies romance, perhaps, either on an individual level (depending on how Crusader Kings-y Stellaris gets) or through laws, but hybrid offspring between two very different alien species? No
And if it did somehow happen a single hybrid is not its own species, it is a cross of two others. A liger, for example, is Panthera leo♂ x Panthera tigris♀, not Panthera ligris. They are not always sterile, but often are. If they are not sterile and multiple hybrids establish a population then they become their own species, the result of hybridization. See: many, many domesticated plants.
https://en.wikipedia.org/wiki/Hybrid_(biology)
Edit: In fact, I'd probably be a little disappointed if interspecies romance isn't represented. I think you're right about species in relatively tolerant societies, in close proximity to one another and with similar concepts of affection, being likely to want to have a go at one another. Adding laws to represent a government's view on such romances could be interesting. It may not be the most strictly realistic, but I think we are expecting a reasonable degree of anthropomorphism in this game, and alien relationships are a bit of a mainstay in science fiction. I wouldn't expect laws dealing with xenosexual marriages, per se, but perhaps the rights of xenosexual couples? Assuming the species is capable of feeling affection as we understand it I wouldn't doubt that it could be directed towards aliens.