I think it should be fine like that in its case. I see plenty of XBOX 360s and PS3s come through all the time and the owner will usually have them in their own bag and some padding instead of putting a bunch of other items on top.

Though you might run into someone who has never seen these consoles on the xray before and they might call a bag check because they'll see the hard drive inside a metal case and say it has to be removed even if they can see that there is nothing else in there.

To be on the safe side, you could take it out and place it by it self since it is a computer.