This was discussed very recently on help-bison, so you might have been aware of this, BTW.
I am, and also that it was never the intention of the Bison project that the files output by Bison should fall under the GPL, just as text files written using GNU Emacs do not.
You are mightly confused. Emacs doesn't insert text magically for you, Bison on the other hand does.
You are also confusing legal issues vs. intention, if Bison inserts code that is GPLed (no extra exceptions) into its output, then the output as a whole must be under the GPL, this includes that the input (which is part of the output) must fall under the GPL. It doesn't matter what the intention of "the bison project" was.
For example, with versions prior bison 1.24 it is illegal to use bisons output to produce a non-free program; but after 1.24 the FSF[0] decided that one should be able to produce non-free software using bisons output, since there were other programs that did the same thing. And hence the license of bison has such a clause to allow for exactly this.
[0]: Note the Bison developers not much say in this, it is the the FSF that decides issues like this for GNU projects. Infact, it would be illegal for a developer to even change the license without permission from the copyright holder, i.e. the FSF.