I know exactly what you're talking about. I've been a nanny in the past, and have dealt with two ultra pass-aggressive mothers. Their concerns are legitimate but it's the way they present themselves, I get it. I think that yes, it is difficult for her to let go of her son and her control. She's expecting you to be HER. I think that asking about his bowel movements is a little much (unless he has a history of having problems) and although she doesn't ask because she doesn't have to - you know she would. If I had a mother like this, I would sit her down and explain to her that you understand her concern but she needs to decide whether or not she trusts you. That her attitude makes you second guess everything you're doing with the children and that's not fair for you, or them. And if she is so dissatisfied with your care, she can go elsewhere. Yes, it may be detrimental for the child to have to move daycare, but they clearly are damaging him anyways by the way theu are smothering him. I had a mother like that, smothered her children beyond measure and I had to tell her straight up that her smothering would actually create more problems for them in the future.
The bottom line is ultimately your sanity. You don't need someone questioning your every move. You're a professional and she needs to trust that or she can go elsewhere.