Since no one else has answered, I'll give it a shot.
General consensus on these forums is that if you are a MD/PhD candidate you need to have a letter from your PhD advisor. If you don't have one, I'm given to understand that it is viewed as a red flag.
That said, based on my experience I would encourage you not to worry. I am not a MD/PhD applicant, but I did have one letter from my research mentor who was a PhD, and it did not seem to hinder my getting interviews at more clinically focused locations. In fact, even at places that give 1 month for research and don't prioritize, they still wanted to talk about research.
My 2 cents: Include the letter. It won't hurt you, and can only help!