I wouldn't say that there's 'confusion' - just that the terms are actually far looser than the linked document would suggest, because many fasteners can be bolts or screws depending on how they are used.

I would say that machine screws are usually used as screws. Machine screws are generally driven with a Phillips/Posidriv or flathead driver into threaded holes, so don't necessarily need a nut, but you can use them as bolts with a nut also. You use a spanner to drive lag bolts and they generally have hex heads like bolts so I would call them bolts, but technically they are actually screws.