Hanging on the bars is a HUGE difference. I see people locking their arms and bearing a significant amount of weight, reducing the work compared to a the same number of steps on real stairs.
The treadmill discussion brought up two differences between the treadmill and a track that seemed important: elastic rebound from the rubber tread stretch, and elastic bounce from the treadmill suspension. If there is a rebound or a lift provided, that will reduce the work. I don't know the mechanism and there are many different "stair" machines. There are differences in stairs themselves, say between a bouncy bleacher, and a concrete stair. I assume people adapt their gait and timing to take advantage of natural rebounds.
I run stairs in a ski conditioning class every fall. I don't currently run stair machines, but years ago, when I tried them, they seemed clunky and a bit odd.
An even larger difference is that in my fall conditioning class, there is an instructor and other people running. I have never pushed with the same intensity as when I am in that group, with those instructors. There is some human psychological benefit to being in a group that is told to do something intense for the next two minutes. You just don't quit. Bottom line: we are all a bit lazy, and it does not surprise me that stair machines get used at less than the maximal work, which would probably be as good as real stairs.