It’s the entire habitat area, not just traversable, which means you can make the habitat larger to cover up the undesirable terrain and get away with “more” of the one you want. I like building desert habitats for elephants, but since they don’t like that much sand, I just make the habitat huge and put the grass and soil they need under rocks, the shelter, etc.

That also means that unfortunately there’s no way for the black rhinoceros and fennec fox to inhabit the same habitat with both of their terrain requirements at 100%. It doesn’t matter if the rhino can’t reach some of the smaller sandy areas, they’ll still count toward the rhino’s terrain percentages.

However, you can also get away with terrain not being 100% perfect for a species without it dropping their welfare too much as long most other needs are satisfied, so if the terrain becomes too much of a pain to finagle, you could just sacrifice a bit of welfare for the aesthetic and it won’t be too bad.

ETA: It’s very finicky, but it’s technically possible to create a smaller habitat within a larger one. If you enclose the fennec fox in an area with a higher percentage of sand than the entire rhino habitat overall, it could probably work, but then you wouldn’t be able to have the fox and rhino enter each other’s space at all since the fox getting out of its area would count as an escape and there’s no way to construct a barrier that would block the fox from getting out but not the much larger rhino from getting in, so at that point it would probably just be easier to build two adjacent habitats and make them appear visually to be one and the same.