It's definitely a concern. The answer seems to be to have more of them, not necessarily wider, and to make sure there is cover and protective spaces along them for smaller animals. here's one study from Canada
Having those predators captured inside a smaller area between major roads whith no safe way of getting out, puts a lot of stress on them to find food. This in turn can make them much more dangerous to humans but also other prey animals. Making a safe crossings will give the predators a chance to expand their territory to a more natural size. Similar examples can be found in India with tigers being caught inside a major road network getting really close to humans.
It’s going to be covered in more than one million native plants!? Are they counting every blade of grass? Most California grasses are non-native. If they manage to have a small patch of native plants the animals might like it too much. They’ll just hang out up there watching the cars go by.
Native plants generally require native habitats to thrive. I have doubts that shallow soils on concrete will support a lot more than weeds. Coyote bush, and maybe a few manzanita might survive. But I don’t think millions of native plants, as was stated in the article, will be sustained by a wildlife overcrossing.