You're absolutely right, licenses are regularly sliced and diced into ultra specific categories. Especially when it comes to the category of collectible (1/6, busts, t-shirts, bobble-heads, etc.) I actually work in the legal department of a "major media company" and I've seen these kinds of license agreements up close and personal.
But in this case, my guess is, it's unlikely that NL/WB licensed out 1/6 figures from only one of those movies. LOTR is generally treated as a single property when it comes to licensing these days. (In the early days, they were separated more because all three movies hadn't come out yet.)
If they wanted to do a smaller, cheaper license, it's somewhat more likely that they'd just limit the number of figures they could make, rather than limit the movie they could be from.
I don't have any inside info on this specific contract, but that's my guess.