Surprisingly, I haven't had any problems with cohabitation. While I was doing the Jurassic Park Chaos Theory mode I accidentally released three Struthis in with the raptors but left them there because I was distracted by other things, but only one Struthi got eaten and that was by the one raptor of the three that had the "Hates and attacks everything" negative trait who was shortly after killed by one of the other raptors. Twenty or so minutes later I get a low health warning and the two remaining Struthis were still alive albeit starving to death and I moved them to another enclosure that had more Struthis. Before that, doing the campaign I was on the last mission and got the Allos and Metrias and put them together and they were fine. Haven't made compies yet, but I honestly feel that the like/dislike system is working pretty well.
Make sure the enclosure is large enough for the larger of the two species to be 100% comfortable in, and try to centralize their forest/rock/water needs in one side or section. That way the second smaller species can have their own area with some or total overlap and feel comfortable as well (aim for 100% comfortable with both, it's actually not too hard to do). Also keep an eye on both's cohabitation stat, even if they like each other they'll still get testy if that stat goes into the red. This also works for species that are neutral to each other, though a somewhat larger enclosure may be needed for them to have a bit more space away from each other. As long as the predator's prey need is satisfied with the goat feeders and they're 100% comfy they should leave each other and herbivores alone. And always keep an eye on the cohabitation stat.
