Your pilot qualification will be determined after you become a cadet. While it is true that the academy use to put a lot more emphasis on PQ status, they are finding that they usually have more than enough pilot qualified individuals; and that while 90% walk into the academy with dreams of flying; only about 50% of the class will actually apply for Undergraduate Pilot Training. The rest will change their mind. New dreams. Don't want to give 10 years of their lives. etc... So don't worry about believing that your chances of getting an appointment will be affected. It won't. Your application simply state "Medically Qualified". That's all they see for now, and that's all they care about for now.
And it is very nice to see comments like Bandit's. AVT, you obviously have the "RIGHT ATTITUDE" towards the academy. Good for you. But there are plenty who don't. Many want to fly, be the first astronaut to Mars, Medical School, etc.... And if they can't be guaranteed that on day 1, they don't want anything to do with the academy. Some even go the first 2 years at the academy to see what the chances are of them getting the job they want. If they see, based on other classes and graduates, that their chance of a certain path doesn't look good, they will quit prior to commitment on their 3rd year. Best of luck. Mike....