Oh I agree about the transponder. From reading the article it seems like two radar systems, with one that tracks automatically after 29,000 ft. So that's what I was referring to. And, I know nothing of his stuff - just quoting from the article. It's an excellent read.
The automatic transponder works at all altitudes, not just above 29,000 ft. The websites that track planes in that area doesn't have the ability to track a plane below 29,000 ft. It has to do with their coverage in the area, which is not good that far out over the sea, not to do with it not sending signals. If you look at the video that we saw the first couple of days, you can see that they had no trouble tracking the plane when it was over land before it reached cruising altitude.