My sense is that it's not much of an advantage, but as long as he knows you well and will write a good rec, I think it's fine that he's not your manager. It is typically important that your manager at your CURRENT job write a rec for you, but you have more discretion with the other two recs. It's always nice to have someone that went to that school that can testify to why you're a good fit, but I don't think it will make or break you unless he's a super big shot alum.
My recommenders are 2 HBS and 1 without an MBA, and that's just a coincidence as I thought they were the best folks based on our relationship and the accomplishments they witnessed. They'll be writing recs for all of my schools, not just HBS, so I will not have official alum recommenders elsewhere.