I do not recommend packing the housing with the camera inside, we tend to think of the housing as a armoured shell protecting the camera, the fact is that if any of the push button or controls where impacted, the force of said impact would be directed to that control/buttons making the camera actually more vunerable. thoses buttons due to their design and location normally are not a target area for impact, having some metal shafts extending it out make it the quite the opposite.
I wouldn't be caught dead travelling this way, instead I do as Deep6 does, use it as a storage bin and stuff it with anything soft and cumbersome.
I regularly travel with my 20D inside the housing, but without the O-ring. I used to use a Lowepro but just switched to a Think Tank (fits my entire macro rig, including 2 strobes; is smaller than the Lowepro and about 3kg lighter - bravo!). The set-up is quite well padded and works fairly well.
And I can personally state that the Aquatica housings are robust enough to survive a 3 foot fall off a table onto concrete, with camera and lens inside, and emerge unscathed (the housing and the camera anyway - the lens snapped in 2). So yes, while I agree that there is a risk if the housing suffers an impact with the camera inside it, I am not too worried about it:
- for one, I dont plan to drop the bag
- second, the bag is quite well padded
- third, housings can be quite robust (my 1 incident above is not statistically valid - still, I have personally dropped my 500/4 a few times; had my 100-400 knocked off a tripod while trying to dodge a charging elephant, etc., so I have a lot of faith in modern electronics' ability to occasionally withstand abuse)
- fourth, if you drop the housing hard enough, you run the risk of damaging your camera's mirror alignment, lens elements, etc. anyway
Still, your point is valid - there is probably an incremental risk if you put the camera in the housing. So why do I take even this small risk? Simple: weight. My carry on gets quite heavy enough as is, so all I carry in the inner padded compartments are lenses, strobes, bodies and housings. Cables, batteries, etc. get chucked into carry o, so there is nothing else in my bag to stuff in the housing. Anything else means either getting a bigger bag, or adding weight to the carry-on. So this is a risk I take.
Btw, I am in Lembeh and just saw the new Aquatica 40D housing. Sexxxxxy in black. As soon as I flood my remaining 2 20Ds, it is time to upgrade. 
Vandit