> deep program transformation
It doesn't have to be deep, does it? You can't transform the entire program, so there's an arbitrary cut-off anyway.
Here is some discussion here on why a pretty serious for GHC stalled: https://www.reddit.com/r/haskell/comments/2s97d0/the_state_a...
In fact, supercompilation subsumes many common optimizations, such as function inlining, constant propagation, list fusion, etc. So we can say that it's actually used "to a small degree", although I wouldn't really call it "supercompilation" per se.
The reason that full-blown supercompilation is not used is that it's too unpredictable -- the direct consequence of being too smart. I've elaborated on it in the final section of the blog post.