I don't know about other states, but here in NJ business owners cannot override local parking ordinances.
There are 2 WalMarts within about 7 miles of each other. Both have signs that say "No Overnight Parking" because both towns restrict overnight parking. The one in my town sits at the end of a vacant mall. The parking lot is expansive and always empty. But no trucks or RVs ever park there, despite being reasonably close to Rt. 80. Somehow truckers know not to park there.
The other WalMart is a bit closer to Rt. 80 and is part of a very active mall with less parking. There are typically lots of trucks and a handful of RVs there overnight. That one becomes a hotbed of prostitution and drug sales after a while and the cops will crack down on the overnight parking rules. Then they'll let it slide again until the scumbags ruin it again. I parked there one night just to say I did it. Sure enough, at one point a car full of lot lizards rolled up and started visiting trucks. They must stay away from the RVs. There was a homeless guy in a van, with a dog, living there for months. He had a sign on his van begging for donations. It was a pretty flagrant violation of the rules but for whatever reason the cops looked the other way. I think what ultimately led to his demise was not the local ordinances but the business owners complaining about his panhandling. I gave him $20 once and saw him at the liquor store buying beer and scratch-off lottery tickets minutes later. Lesson learned.
Now that I've typed it, I don't know what the purpose of my story is. I guess it's that in most cases it's not up to the business owner whether to allow overnight parking and that enforcement varies place-by-place. The "No Overnight Parking Signs" are often cover-your-butt moves by the businesses. And, like others have said a few bad apples ruin the courtesy for everyone else.
And I don't get why you'd ask the manager. First, it's not likely they have any authority over parking anyway. Second, it's far better to do it and beg for forgiveness later than to get a flat out "no" and have to find somewhere else.