As a veteran of many reverse engineering and cloning projects, I think that, absent insider information, you cannot realistically reverse engineer and clone a commercial dough/pizza in a reasonable time frame without numbers. Numbers means weights, dimensions, nutrition information and ingredients lists from which the pecking order of the ingredients, by weight, can be ascertained. Concentrating on flavors and color is subjective in nature and, in the abstract, can mean endless experiments to achieve the desired end results. Moreover, flavors and color are largely a function of the precise ingredients used. Often these ingredients are not available to the average home consumer at the retail level. The best marriage is to come as close as possible on the dough formulation and the ingredients actually used to make the dough and the rest of the pizza that is to be cloned.
On the matter of the flour, when I researched that specific ingredient in the context of the MM dough, I saw references to the flour being 1) a high gluten flour, 2) a Vitamin E enriched high gluten flour with wheat germ, and 3) whole wheat flour. I think it is safe to rule out whole wheat flour because, while containing the E Vitamin (alpha tocopherol), and while containing wheat germ and a fairly high protein content (in some cases as high as 15% or more) that can contribute to dough and final crust color, whole wheat flour does not have the gluten forming characteristics of most high protein refined white flours and it cannot yield a dough with the forming, stretching and tossing characteristics as shown in the videos referenced earlier.
Wheat germ by itself, whether raw/crude or toasted, contains a fair amount of Vitamin E (see, for example, the Nutrition Facts for the Kretschmer toasted wheat germ supermarket product at http://www.quakeroats.com/products/more-products-from-quaker/content/cereals/kretschmer-toasted-wheat-germ.aspx
). By contrast, regular refined white high gluten flour, while enriched with various B Vitamins, does not contain Vitamin E (see, for example, the specs for the General Mills All Trumps high gluten flour at http://www.gmiflour.com/gmflour/flour.aspx?type=Espring#50121
). If the above analysis is correct, then a Vitamin E enriched high gluten flour with wheat germ seems to me to be the most logical combination of ingredients.
As the MM chain expands, it would also be entirely logical and natural for the flour used by the various MM stores to be a blend made especially for MM. It is also possible that, if the molasses is in dry form, it also can be included in the flour blend (actually a pre-mix) along with yeast (if IDY) and salt. In a home environment, you would have to experiment with blends of wheat germ and high gluten flour and molasses and introduce the yeast and salt in the normal manner.
The increased dough coloration that some writers mentioned can come from the wheat germ and the molasses used by MM in its doughs. Since the MM red sauces do not contain added sugar (there are natural sugars in the tomatoes used to make the sauces, however, and small amounts in mozzarella cheese), this is one of those instances where having the Nutrition Facts for the MM dough would give us a rough idea as to how much molasses is likely to be used in the dough. It would help, of course, to know whether the molasses is in liquid or dry form since that can also affect the math.
Malt, both in liquid and in dry form, and nondiastatic in nature, has been used before in commercial doughs. A good example is the early Sbarro NY style pizza dough. I have used the liquid form of malt and it will add color to both the unbaked dough and the final crust and crumb. If liquid malt can have that effect, then molasses should have a similar effect. I would stick with the molasses for your experiments.
EDIT (4/15/14): For the most recent link to the GM All Trumps flour, see http://professionalbakingsolutions.com/product/all-trumps-enriched-flour-50-lb/50111000
EDIT (9/1/14): For the Wayback Machine version of the Kretchmer item, see http://web.archive.org/web/20120106133435/http://www.quakeroats.com/products/more-products-from-quaker/content/cereals/kretschmer-toasted-wheat-germ.aspx