I'm not understanding this. If the cooked meal is more than what the frozen meal says the calories are, then you are 'deriving those calories' from more weight showing up on the scale when you weigh the meal, cooked. I'm thinking that the heavier weight is due to water that has melted into the cooked meal, the water having come from frosted food (water is zero calories). So, where are extra calories coming from? I don't think there are calories being added. Just water. This assumes that the calories listed on the box are correct - and you're right, they are usually close enough.... the nutritional values are calculated from the production process (the manufacturer has some stake in making sure that portion sizes are accurate - portions mean money to the manufacturer).
The water, I guess, would come from the freezing process.
I sometimes make frozen meals from homemade, and the texture does change when I look at the thawed or thawing product. Mainly because water has accumulated on the surface of the mashed potatoes, for example, and then the method of cooking determines what happens to that water (does it bake off in high heat or just get reabsorbed? depends...)
However, what I put in the foil pie pan doesn't change as far as calories go, that I am sure of!
That's my reasoning about frozen foods. I just go with what they say. Sure, there's variation, but, like money, the producer has a strong interest in keeping the portions uniform.