If your boss says apply. Then apply. From my experience when you are applying for a different position within the company, your experience in that company trumps the degree. If you were to apply to that same position in a different company then the degree trumps the experience. Again I will go back to something the Human Resources departments are in love with today. that is Core Competencies. Google it. They are trained to interview to find out what your CC are. This is almost all that matters these days.