He's the Director of my lab and an associate professor at a local school of medicine. Surely, a guy like this will make me look good if the LOR is well written.
If you have already made up your mind, we can stop this discussion?
If instead you are
asking a question, it should be "What is required of a LOR for medical school?" or simply put "What do adcoms look for in a LOR"?
Here are a couple of things that come to mind:
Objectivity
If there is a conflict of interest, you shouldn't even ask. And if you DO ask - he should decline (especially him - since he is at a medical school he should be acutely aware of how LOR writing works).
You see, objectivity is a
cardinal requirement of LORs. This is why there is a process that ensures confidentiality of the letter. Do you think sometimes letters are submitted that are negative and don't recommend that the applicant get in? You betcha. Adcoms want objective assessments.
In your case, he's in a relationship to your dad. Do you think that he can be objective? Hint: that's pretty much a "NO". This has nothing to do with his sexuality or the legality of his marriage or whether you consider him your stepfather or even consider him a toaster. He cannot be objective. End of story.
Authority
This isn't "look at my title and what I do" kind of authority. I mean "the capacity to evaluate you". This is a person in a specific relationship to you: a boss/PI/professor (please note that a "professor" isn't automatically a person who can write you a letter - they actually have to teach you! This point seems lost on some people).
Also, titles do not impress adcoms by themselves. What I mean is - a "good letter" doesn't require a great title. And an impressive title doesn't make up for a crappy LOR. Hell - most everyone on the adcom will be a professor at the school - how impress will they be?
Now - there are many other aspects to great LORs. But for now, you get my point. Let's for a second say you and him both commit an acts of omission, and don't have him explain his relationship to you. He STILL can't specifically discuss your performance in a class setting or a research lab setting. Do you see what I am saying? Even then - this LOR really isn't going to help. At all.
I'm pretty sure legal status doesn't really matter here. You're supposed to get letters from people who can professionally evaluate you ...
This. Like I was trying to state before (albeit on my phone so I couldn't be so verbose) - this person is NOT your professor NOR your PI / Boss. This entire discussion is moot. You shadowed him. This will not replace the required letters for almost any school. IF you want a favor from him, have him pull some weight at his school and get you an interview and lay it to rest. Finally having him write a letter reflects poorly on your decision-making faculties.