Cholesterol, despite its reputation for causing health problems in excess, is an important molecule in the functioning of our bodies. However, cholesterol is not an essential nutrient. Our bodies can produce enough cholesterol to meet their needs, and so no cholesterol need be included in the diet for health. Complete food recipes usually include zero cholesterol.
Enzymes, in general, are molecules which allow a certain type of chemical reaction to occur. Digestive enzymes are enzymes which enable certain types of molecules to be digested -- i.e., broken down into forms which the body can absorb. For example, amylase is the enzyme which breaks down amylose, the indigestible component of starch, into digestible sugars. It is therefore necessary to digest starchy foods such as grains. Lactase is famously the enzyme which breaks down lactose into glucose and galactose. Phytase is the enzyme which breaks down phytic acid, neutralizing its antinutrient effect.
Digestive enzymes can be useful to include in a complete foods recipe, to assist in the digestion of the recipe. For example, a recipe which includes large amounts of a starchy ingredient such as oat flour could usefully include amylase, to assist in breaking down the starch. A recipe which includes large amounts of a phytic acid rich ingredient (again such as oat flour) could usefully include phytase, to assist in breaking down the phytic acid.
Probiotics are supplements of bacteria. Bacteria in the gut serve an important physiological and digestive role, and the purpose of probiotics is to increase this population of beneficial bacteria. Some people have expressed concerns that complete foods do not adequately feed the gut bacteria, and could result in a reduction in its population. This concern may be unsubstantiated, assuming that the complete food contains an appropriate source of fiber. But in any case, a person who was worried about this happening could choose to include a probiotic supplement in their complete food.
"Phytonutrient" literally means "plant nutrient," and it is a catch-all term for chemicals in plants which, though not essential nutrients, may nonetheless have health benefits. For example lycopene, a chemical abundant in tomatoes, has been found to reduce the risk of some types of cancer, and is therefore a phytonutrient. Plants contain millions of chemicals, largely unstudied, and any of these may potentially have health benefits. The lack of a diverse profile of phytonutrients has been cited as a potential nutritional defect of complete foods.
Happily, there are such things as phytonutrient supplements. Generally these consist of dried extracts of a mixture of plants which are believed to be especially healthy and packed with nutrients. See here for discussion. Anybody who was concerned about not getting phytonutrients could take one of these supplements.
"Nootropic" is a catch-all term for chemicals which are believed to enhance mental functioning beyond its normal level, for example increasing alertness, memory, intelligence, etc. See Wikipedia for a list of potential nootropics. People who believe in their efficacy might wish to include them in their complete food.