Ok, I finally figured it out (whew!). The cause is the encounter zone mods I had installed (Arena and MEZF - Missing Encounter Zones FIXED). Once I disabled those two, Alduin starts fighting properly.
SOLVED: @Greg, you were correct. It turns out that in fact it was the script mismatch I mentioned in my previous post, and it was baked into the save game. Unfortunately, in order for the fix to take effect you need to start a new game (so if anyone in the future runs into this, sorry, your current save is probably SOL).
In any case, after removing the script mismatch and starting a new game, Barbas appears in the correct place and Ill Met by Moonlight proceeds correctly after talking to Sinding the first time.
KLWaster's post in Dragon in DLC2MQ05 won't attack or aggro -- Now also affects Alduin in MQ206 was marked as the answer