Agreed that your ticket isn't protected but it does take all of a few minutes usually to transfer, versus the 30-60+ minutes to clear immigration/collect bags/check in/clear immigration again. So with my 3-hour layover, if the plane had been delayed an hour and my bags had been checked through, I'd have been fine - no sweat. Go to the transfer desk, check in and all is well. But as Qantas closed check-in 90 minutes prior to leaving, if my bags weren't checked through, making that would have been very tight if my bag had not come out quickly (and reports I'd read said it could take 45+ minutes). So it does make a big difference as to your likelihood of making your next flight.

Of course it's ultimately my fault for having made the booking. I didn't calculate the difference correctly (in my mind there was a 5 hour gap not a 3 hour gap - I usually leave 5 hours for connecting international flights on separate tickets). I got lucky and had no problems but I WON'T be tempting fate again!