You’re right; there definitely seems to be a benefit to combining casein protein with C3G, as detailed in this article.
The recommendation to take Indigo-3G on an empty stomach is probably due in large part to initial concerns about larger amounts of fruit potentially interfering with the absorption of C3G.
While I don’t know to what extent that may play a role now, Indigo-3G has been designed to enhance overall absorption, even when used on an empty stomach.