It works for me (the spell part, didn't check the AI). Maybe you're confusing Great Generals and Great Commanders? The former are only present with Advanced Tactics on, I think, and work just like in vanilla BtS. The latter cannot lead units by themselves, but other units in the same stack can cast "Join Great Commander", which works about the same. Incidentally, Great Generals can also join Great Commanders, giving you a strength-1 unit; that ought to be fixed.
And yes, it's stupid that there are two types of units for this. ExtraModMod merged the two, but I reverted that change for some reason I don't remember. It's possible that the AI can use Great Generals, but not Great Commanders.