The way I understand it is, a main roof on a building is the roof that covers the most area of a building, or the largest roof at the top. It's usually the first "roof" that you come to from the ground, not counting podiums or setbacks. So in priller's drawing below it would be the largest roof on the building at the top.
And yes, typically the mainroof does cover up the highest occupied floor. But I think 360 is a special case where the 44th floor, (highest occupied floor), actually sits on the mainroof. In priller's drawing you'll notice a level up there above the mainroof. I believe that is actually a residential floor. I think that's the reason why there's only a 2 inch difference between the main roof height and highest occupied floor height. Above that floor is another level (the one with a sloped roof), however that one is mechanical. Greg called that level the 45th level. At Emporis, and a few other such databases, officially floor numbers are counted only by counting occupied floors and mechanical floors that are contained within the main structure of a building, in other words below the mainroof. Any levels that are inside a mechanical penthouse are not included in floor numbers. Although some people argue that mechanical rooftop levels should be included in the official floor number, I sort of am in that group. It gets trickier with very tall buildings since many of those have multiple mechanical levels even halfway up the building for air conditioning, water pump stations and elevator equipment. The Sears Tower is an example of this. Most listings for the Sears Tower show it to be 110 floors, (Emporis does not), this is because the mechanical penthouse at the top takes up 2 levels. This is where I kind of disagree with not including mechanical levels, because even though those two mechanical levels that sit atop the mainroof aren't included in the floor count, the other mechanical levels lower in the tower are! Infact, the 103rd floor of the building is the highest occupied floor. There's actually 7 levels above that that contain mechanical stuff, and only 5 are counted in the floor number. The other two are the two levels in the mechanical penthouse.
Here's the Sears Tower's page at Emporis. In the fact listing you'll see the notes about the mechanical penthouse not being included in the floor number, 108 floors instead of 110. And you'll see a fact about the 103rd floor and mechanical levels above it.
http://www.emporis.com/en/wm/bu/?id=searstower-chicago-il-usa
As for top floor heights, (highest occupied floor), and what they're measuring, they always are measuring the floor slab height. So if you're standing on the 44th floor in 360, you're feet are at 462 feet 1 inch off the ground.
And about the height discrepancy 563 feet vs 581 feet. I really don't know. I'd like to know that myself. As you pointed out, why chop off 18 feet of spire? Surely that couldn't have cut the cost down all that much, and we all know it's not for zoning reasons since city council has been cool with taller buildings.
I'd also like to find out what the height is for the parapet on the mainroof. I really like to get as many heights as I can for a building as to leave out any doubts of the heights.