Suffix arrays are useful for approximate matches too-- they're used by the binary delta program BSDiff[1] to match similar code sequences. BSDiff is used in Google products (Including Chrome)[2] and Firefox's delta updates.
Courgette isn't BSDiff, it is Google's replacement for/improvement upon BSDiff. They were using BSDiff for Chrome updates before they switched to Courgette.
Courgette is a preprocessing stage to reduce the number of differences (disassembly + offset fixup + reassembly) plus BSDiff to catch anything else (using lzma instead of bzip2).
[1]: http://www.daemonology.net/papers/bsdiff.pdf [2]: It performs additional preprocessing to make updates smaller (Courgette).