I'm likely getting out of my depth here, if I wasn't already
but the examples show pictures-only layouts. If we're talking about forums as well, where text has to be fitted in, then perhaps (Dave would know the answer) variable thumbnail sizes would mess up the rendering? I do remember from when I worked on web pages more than I do now that the page loads better and faster if the image sizes are pre-defined in the code because then the browser knows how much space to allot and starts rendering the page before the images completely load (which makes a difference especially on a slow connection).
I know what you're saying, and I've used non square thumbnails myself on at least one of my own web pages, but it's not a dynamic page like those on ATP. I have no idea how difficult it would be to enable us to pick which section for a thumbnail or enable us to upload our own thumbnails or whether the majority of users would take advantage of this if it was reasonably doable.