There are actually some mycoparasites that have been found to be useful in preventing root rot. If these mycoparasites are in the water, the second that there is any Pythium, these parasites would remove it. It is called parasitism. I believe that SubCulture has these parasites in it, and that is why it helps prevent root rot.
If something helps to get rid of root rot why would it not also prevent it? If we are to follow your logic, than these statements would be true. "If your air filter in your car is clogged, you lose power. If you change your dirty air filter, your power comes back. But if you change your air filter before it becomes clogged, you will not prevent the lose of power." Obviously, this is false.
This is the same thing that is going on with the root rot. It is brought on by a parasite (or fungi as its commonly considered) in the water. If, when this fungi is in full swing, SubCulture will help to get rid of the parasites in the water when they are in high numbers, why wouldn't it get rid of them in smaller numbers as well? It seems as though it would be easier for the colony of "good" stuff in the water to kill a small number of "bad" parasites than it would be to kill a larger number once the rot has taken hold.