I can't stand freeze dried foods anymore. Last time I tried to subsist on Mountain House for five days I wound up with no energy at all by the end of the trip.
So my wife and I have been evolving our backpacking diet away from that stuff. We save plenty of money this way, have much more energy but yes, our food bag may be marginally heavier.
We've experimented with various couscous and couscous/polenta mixes with some success, and recently we discovered this stuff –
http://www.bearcreekcountrykitchens.com/soups.php
Bear creek make soup, rice and pasta mixes. The rice stuff seems to pack the most calories.
It was on sale at a local supermarket so we got a bunch. I mostly select 'em based upon cooking time and calorie amount.
Finally, we'd found a packaged food that came in sufficient quantity to satisfy two hungry hikers!
We start by drying some sort of meat over our wood stove. This is store bought chicken breasts but we also dry fish and venison –

The meat is broken up into small bits and bagged. Don't dry it too much! It wants to be like a soft jerky.
In camp, I throw the meat, Bear Creek mix and water in a pot and heat it over my trusty Trangia stove. I don't bother to bring it to a boil, just good and hot.
But what I do is take the food off the stove, put my smaller pot on with a quart of water and two tea bags in it, set that on the stove and put the food pot on top with the fry pan / lid on top of everything.
The tea also need not boil, just heat up to 180 degrees or so. Since the tea bags were added with the cold water the brew is strong and ready to drink.

That is Bear Creek creamy potato soup that I've added a bunch of home dried fish to.
The pot holds 1.75 liters, so that is a ton of food. I think I used the amount of water recommended, but as you can see the result is thick enough to stand a spoon up in.
Package says "Serves eight", but my wife and I ate the whole thing, just.
I know that most UL hikers would never consider taking a second pot much less a full Trangia setup, but I find stacking the pots to be a great way to finish cooking the meal while making a pot of tea or coffee.

So anyway, in direct response to your original question ( finally! ) I'd recoemd adding the rice/pasta/soup mix to the cold water, then heat it over the stove, then remove it and place it in the cozy.
My experience indicates that it will cook much faster this way.
Why waste the time it takes to boil the water when the food could be rehydrating/warming/cooking all the while? And the food need not be brought to a full boil.
– And if you have a second pot that fits under the first, you can even make a pot of tea with the food perched on top, sharing the warmth. You'll get piping hot food and tea at the same time!