I may be misreading, but the issue is that some of the elisp sources of CEDET were generated from bison input files automatically at some point -- but they're still elisp sources; a user can still modify them if needed, and if an asteroid hits the house of whoever did the original conversion, development can still continue that way.
That doesn't mean that _technically_ we wouldn't be a lot better off if the bison sources made it into the next emacs release, for completeness and ease of future development -- but I'm not sure I see the GPL violation here.