Coaches offering scholarships value credible references. It is particularly important in situations like yours where the coach has limited access to seeing the player in person, which they prefer to do multiple times. I would absolutely look to use this reference if the reference thinks it is a fit. I would have your son talk to the P5 coach, tell him about the mid-major he is talking to, ask if he thinks it is a good fit and if the answer is yes, ask if it would be OK to list him as a reference when speaking with the mid-major coach.
There is no conflict because the P5 already told you their slots are filled, at least at the present time.