Mix eggs, cream of mushroom soup, and milk together in a bowl and set aside.
Boil penne pasta in a large saucepan with a pinch of salt until al dente and cool slightly; don't completely cool. Pasta can still be warm. You can use whole grain pasta if you prefer.
Place cooked pasta in a large casserole dish or aluminum casserole pan.Add 2 sticks of butter to warm pasta and mix well. Add egg and milk mixture and mix well turning slowly. Add all purpose flour to pasta and blend. Season with seasoned salt and black pepper. Added shredded cheeses and mix slowly; make sure cheeses are evenly distributed throughout pan of pasta, mixing one area at a time. Leave 3/4 cup of cheese as a topping before placing in oven. Sprinkle in nutmeg and mix into pasta. You'll need a large heavy spoon as pasta will be harder to mix. Sprinkle top of mac and cheese with the last 3/4 cup of cheese and place in a preheated 350 degree oven. Bake for 40-45 minutes or until cheese is melted and a little brown on top.