Well, she's the mom so I would say she gets to decide these things. Not sure why you have a problem with that.
When my kiddos were 4, if I left them overnight with someone, it was to help me out. They would rather stay with mommy and daddy than stay with anyone else, so it's not for them that they go stay with others.
So if she's not putting your needs above the child's (or her own) .. I don't think that's so terrible. She's a mom.
Maybe she and hubby have concerns about yours or your hubby's driving or how well you'd strap him into a car seat? Hard to say. It's really not a big deal. It may just be easier for them to do the driving.
As for looking after bathroom time, it probably dates back to potty training, and it has stuck in his head since then since probably not that long ago. I know when I was training mine, only myself and a couple of people were entrusted to our method - because it was simpler to keep to our 'method' and everyone was on same page. I would guess (?) since none of us can tell you, that's what he is regurgitating.
If you have issues with your DIL (and it sounds like you do), I'd either move past them, or deal with them - counselor, talk to your DIL, etc. It doesn't do any good to make yourself out to sound like she's being unreasonable. She's just a mom putting her son's needs (and her own) first and that's ok. I wouldn't take it personally.