In my opinion an airline pilot could only ever be over qualified if they were a 747 AND A380 AND ex Concorde test pilot with 50,000 hours. The simple face that you have a degree in the aviation field does not qualify you in any way to fly an aircraft. Sorry to sound brutally harsh but, in my opinion, any pilot that thinks they are over qualified for the job is dangerous.
I did my training with a guy who used to work in aerodynamics and it's fair to say that he had to unlearn a fair bit for the JAR exams and yes he nailed PoF and performance with 100% (but then so did people who had come straight out of A-Levels) he struggled with the raw handling skills in the IR phase and also in the multi crew conversion stage.
In terms of you starting "late" I think you can justify that easily enough at an interview, you have good reasons for not jumping straight into training right now - and it will certainly look good on you if you are doing something worthwhile during that time, like studying for a PHD.