I read the other thread in the link and all the posts in this thread, and I don't see anyone mentioning the reason the original bolts are made with that weird shoulder they have.
In the locations where the bolts go through the bed, they also go through the braces welded to the underside of the bed. The shoulder looks like it's slightly shorter than the height of the brace. I believe they cranked down on these bolts at the factory till the shoulder contacted the top of the frame. This gave the correct tension to hold the bed to the frame without collapsing the brace.
I too have used regular bolts, and had no problems so far. But it's something to think about, I would not crank down on the regular bolts too hard, you might collapse the bed brace. I never looked at it really, but it may be possible to slip a piece of pipe inside the braces if you were concerned about it. I wonder if the later model bolts that were mentioned in the other post have sleeves made into the braces? Or maybe that's why the speed nuts "weld" themselves like was mentioned. Maybe they torque them just enough not to collapse the braces, and then they lock themselves in place.
A couple of trucks I have owned had banging noises in the bed area when going over bumps. I found someone had dropped something in the bed, collapsing the brace under the bed a little bit, and then it would bang on the frame as I went over bumps. The regular bolts actually fix this problem. Or you could add a washer on top of the frame.