Looking for an accurate nutrition database

The answer is that they are not much different.

During fermentation, some of the milk's lactose is converted by bacteria into protein and other substances. The amount of conversion is pretty insignificant in terms of calories and grams of macronutrients. The most important effects are the changes in taste and consistency and the presence of live bacteria. Usually many of the bacteria survive the highly acid stomach fluids to reach the small intestine where they continue digesting lactose.

Fitday.com gives the info below for a cup of each, which may be surprising at first. However, commercial yogurt tends to be more dense than milk, as you might see if you make it at home: a cup of milk gives you some watery fluid floating on top of less than a cup of yogurt.

Food              | Calories | Fat  | Carbohydrates | Protein
------------------+----------+------+---------------+--------
Whole Milk Yogurt | 149 kcal | 8.0g | 11.4g         | 8.5g
Whole Milk        | 146 kcal | 7.9g | 11.0g         | 7.9g

If an item of food is stored for a long time, the nutritional values might reduce. Other processes such as freezing, thawing and cooking will also have an effect on the nutrition. Thus the figures given on the box are correct at the time of packaging. The figures at that time might be different from when you actually get to eat the food. In the case of your macaroni, it could absorb or loose water while in storage so the % values would only be correct at the time of packaging. Thus "as packaged" is a reference to the time of packing not the packaging itself.

As to the low fat content, dried powdered foods usually are low fat as it is difficult to make the powder with fat. They will probably have used a hard, low fat cheese such as Parmesan, or a cheese flavouring, rather than Cheddar.