as others have stated Atkins is a high fat-low carb diet. Fat is necessary because it's the ratio of fat to carbohydrate that gets us into the ketogenic process.
Taking Alli really defeats the purpose of eating a high fat diet. As you wrote, it prevents the absorption of 25% of the fat you ingest. So if you ingest 50 grams of fat daily, then 10 grams do not get absorbed. 10 grams is equivalent to the amount of fat in about 12 ml of olive oil. So you could get the same results from eliminating 1 tablespoon of added fat from your diet as you would taking the Alli pills.
Also, when you move to OWL Phase and begin added carbs, your fat intake (the percentage of fat in your daily menu) naturally decreases provided you keep your fat intake constant. The mistake many people make during Atkins is that they add more fat to their diets as they add more carbohydrate. And they stop losing weight.