Getting the mold to grow into the rice is all about moisture, as that's what the mold wants. We often hear about the wash/soak/steam steps, but it really should be wash/soak/dry/steam. A lot of breweries wash and soak in the evenings, let the rice dry overnight, then steam in the morning. The key here is that the outside of the rice dries out while the inside of the rice still retains water. Another part of getting the mold to grow into the rice is humidity in your koji chamber. Think about growing koji in two stages, where the first 24 hours is to get it to grow onto as many rice grains as possible, and second 24 hours is to grow into the rice grains. The first day, humidity is good, as that will help it the mold propagate. The second day, humidity isn't so good, as if it has all the moisture it needs on the outside of the rice, it has no reason to grow inwards where the water should be.
An also important note is the rice hardness. If the rice is too hard, the mold will have difficulty growing into it. This could be due to not soaking/steaming properly, or just the grain variety. In my opinion, the Calrose rice most US brewers use is too hard to make good koji from. Sure, you can make koji with it, and even make sake that is good with said koji, but the koji made with Calrose probably won't be as good in quality as if you had used another rice like YN or Koshihikari.