Just to clarify there isn't any misunderstanding that the E-4 was fitted / designed for the Tomcat. Simply that at the moment the Devs have sources that state the baseline E as well as E-2 and E-4 are all possible. So for the same reasons it does not have AIM-9L just yet, the developers chose the base E model for the time being. As I said, a report would be welcomed it there is direct confirmation it could not actually carry anything other than E-4, but the current sources just confirm E-4 was designed for aircraft like the Tomcat and the E-4 was fired from it.
Considerations for later variants may be made later on.