There’s a chance you won’t be looked at....at all. Many people with excellent qualifications don’t get the call, for whatever reason. Why wouldn’t you apply to a program that offers to put you in front of the people who make the decision? I had my apps in for years, with multiple carriers. Went to job fairs, did all I could. Never heard from the Big 6. The CPP gave me a chance to get in front of the people who do the hiring. The rest was up to me, but just GETTING the interview can be harder than you think. Unless you have military flight time, you can’t count on your phone ringing. Accumulating hours at the regional won’t be enough.
Back to your original question........maybe they won’t look at you negatively, but they might ask. What are you going to tell them your reason was for not applying? Do you think that answer is going to sway them one way or another?