It's pretty obvious that, at the very least, these specific benchmarking apps are given a hugely unfair advantage, and probably only based on internal app ID strings. Apparently the frequencies were boosted for one of the benchmarking apps even if it was just sitting idly showing a menu or something.
Yea, that much is clear. And the AnandTech article (which probably should be the one on the HN front page if it hasn't popped up there since I last looked) is clearer about some of the things they ran to establish that 480 MHz is the norm. I still wasn't sure from that article, though, whether the games and such were run with the device connected to power, whether there are other user-tunable power saving settings that could affect it, etc.
My only point is that I personally feel that more investigation is needed in that direction before I'll feel very negatively about the story. If it's a rarely used but possible mode, it seems like it's on the same level as disabling power saving mode when running a recognized benchmark. I kinda expect benchmarks to represent the peak attainable performance, even if it's not the typical performance.
My reading of the AnandTech article was that the CPU was boosted to max speed for the benchmarks, but the GPU was over-clocked past what normal apps had access to.
