Well, your quite correct my friend and found the culprit on why the system sucks.
While it gets some lucky hits like red and fallow deer or orangutans and otters, in general it disregards many combination that make sense and work in real life just because the animals cant meet each other in the wild, something that should have no matter for if animals like to be around each other.
The current enritchment bonus would make much more sense as a visitor education bonus with something different actually based on animals interacting with each other for animal enritchment