The reason this calorie calculator is asking your your body fat percentage is to assist in calculating your Basal Metabolic Rate (BMR) which is the amount of energy your body needs to maintain itself when you are not doing anything. Muscle tissue is much more expensive for the body to maintain than fat is so if two people weigh the same, the person who is leaner will be able to eat more without getting fat. Only two of the research models use your body fat percentage: Katch-McArdle and Cunningham. The other two research models just assume an average bodyfat.
Most people who think they know their bodyfat accurately really don’t. Despite everyones claims, the electronic body fat measurement devices available online and at gyms are notoriously inaccurate. Unless you have measured your body fat yourself using a skinfold caliper as described here, you do not know your bodyfat accurately enough to use the Katch-McArdle or Cunningham equations.