The rational is that each firearm on the roster has to be submitted by the manufacturer to the California DOJ for drop testing, and the process is expensive. The way the law is written (or the regulation), each permutation and combination must be tested separately, so manufacturers generally can't justify submitting every model variation they offer for the testing. They pick the models they think will sell most/best.
A 1911 in 9mm is not most people's first choice, and I'm sure Wilson Combat had to look at how many they might actually sell in California against what it would cost them to get it added to the roster. If they had thought the numbers would work, I'm sure they would have done it.