There are several ways to make frozen dough. For example, you can make your dough as you normally do, using your regular dough recipe without change, and then freeze the dough immediately (after dividing and scaling). Alternatively, you can let the dough go through its normal fermentation process and rise, and then freeze it. These are essentially the two methods discussed in the Cook's Illustrated article as I read that article. The Zeak article goes a step further on freezing the risen dough by giving examples of fermentation periods (4 hours at room temperature or up to 48 hours cold fermentation). As between these two methods, the dough frozen without any fermentation is not bound to be as good as the other method because freezing kills some of the yeast and, as a result, impairs yeast performance. This leads us to a third method. That method is to make the dough up front with the intention of freezing it right after making it. For this method, you want to dramatically increase the amount of yeast to compensate for the fact that freezing the dough will kill some of the yeast. There is no need to ferment the dough before freezing it (but see below for a related discussion). That is what Jeff Zeak discusses in the last paragraph of his article. It applies to only the third method mentioned above.
When I make frozen dough, I use the third method (increasing the amount of yeast in the recipe). I also use cold water. Norma has used the second method when she has leftover dough at market and the third method when called for by the recipe. A good example of the third method is the Mellow Mushroom dough that calls for freezing right after it is made.
The idea of flattening dough balls for freezing comes into play when a lot of dough balls are to be made and frozen, and where freezer capacity may be somewhat limited. Flattening the dough balls speeds up the freezing process and, once frozen, allows them to be tightly and densely packed together into freezer bags until ready to use. With this method, the dough balls are often subjected to about 20-30 minutes of rise at room temperature before freezing to make it easier to flatten the dough balls before putting them in the freezer. Typically, the flattened "pucks" are coated with oil and placed on wire racks or screens in the freezer and frozen completely through, not just at the surface. Then the pucks can be put in freezer bags as mentioned above. The Zeak article discusses an alternative method in which the dough balls (round) are put on trays or in dough boxes and cross stacked in the freezer and then down stacked. Presumably, there is adequate storage capacity to use this method.