I was a Ranger in 2010 and I know for a fact that the water required is 2 cups per package. Starting in 2010, Philmont changed almost all of the dinners from Richmoor to Mountain House. Maybe what you have been reading is from years prior to 2010. Two Richmoor dinners, the Mexican Fiesta and the Chicken and Rice were still being issued last year and they require significantly more water than the Mountain House and will require a larger pot. Also, there is a breakfast that requires cooking. The trail menu is subject to quite a bit of change between seasons and by the time you set off on your 2012 trek, who knows what the case may be. Philmont is usually very helpful and I'm sure they would provide you with a list of the meals if you called and asked for it.
As for the Mountain House meals, the only difference between the Philmont Mountain House and the Mountain House you buy at the store is the package. The Philmont variety comes in a non-resealable, white plastic pouch and you CANNOT put boiling water in them. The material is thinner than a regular bag and it might break open if you try to rehydrate in them. Also, during training they told us that these bags have not been tested and they don't know what kind of chemicals could be released into your food if you try rehydrating in them.
So, like you said, your 12 person crew would need to boil 12 cups of water for most dinners and one breakfast. As suggested, you might boil a little less water and add more if needed. Also, your food will taste much better if you rehydrate in the pots and let it simmer for a bit, instead of trying to do it in your bowls, unless you like partially hydrated food.