If you want to live dangerously, you can edit the AkInitializer.cs code so that it will only initialize once. Just add a private static bool to keep track if it's initialized, then check that before the call to AkSoundEngineController.Init is executed, and only call it if the boolean hasn't been set, then set it to mark you have already initialized.
However this is a bad idea, since I really don't know everything AkInitializer is running the repeated init calls for, and it could be counter to some Wwise requirements and create more and more problems elsewhere - this is why I reverted all my changes to the class, to make sure I didn't break more stuff elsewhere, since we were still getting multiple issues across the whole project, and am now looking for help on this Q&A forum to get a proper solution.